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Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.

Human satellitess(HSats) are pericentric, tandemly repeating satellite DNA sequences in the human genome. While silent in normal cells, a subset of HSat2 noncoding RNA is expressed and accumulates in the nucleus of cancer cells. We developed a FISH-based approach for identification of the distribution of three subfamilies of HSat2 (A1, A2, B) sequences on individual human chromosomes. Further, using the HSat subfamily annotations in the T2T completed centromere satellite (CenSat) sequence, we isolated, defined and mapped differentially expressed sequence variants of nuclear-restricted HSat2 and HSat3 RNA from cancer cell lines and heat-shocked cells. We identified chromosome-specific and subfamily-specific expression of HSat2 and HSat3 and established a computational pipeline for differential expression analysis of tandemly repeated satellite sequences. Results suggest the differential expression of chromosome-specific HSat2 arrays in the human genome may underlie their accumulation in cancer cells and that specific HSat3 loci are upregulated upon heat shock. [ABSTRACT FROM AUTHOR]

A 14-year boy is given a microscope by his parents. It is not a toy – but a real microscope. He deploys it to rediscover the biology he had known before, but now in a magnified world. With extraordinary intellectual gifts he then, and manifestly later becomes absorbed by the idea that all this, however mysterious at first glance, might be subject to rational understanding, with painstaking study. Thus, was the genesis of one of the greatest cell biologists of the 20th century, Joseph Grafton Gall, who died 12 September 2024, at 96. He had been professionally active up until only a few years ago. There was no one like him in the modern era of cell biology and there will not be another figure like him anytime soon. [ABSTRACT FROM AUTHOR]

Accumulating evidence suggests that the nuclear envelope (NE) is not just a target, but also a mediator of apoptosis. We showed recently that the NE protein nesprin-2 has pro-apoptotic activity, which involves its subcellular redistribution and Bcl-2 proteins. Here we further characterize the pro-apoptotic activity of nesprin-2 focusing on its redistribution. We assessed the redistribution kinetics of endogenous nesprin-2 tagged with GFP relative to apoptosis-associated mitochondrial dysfunction. The results show apoptosis-induced GFP-nesprin-2G redistribution occurred by two different modes – complete and partial, both lead to appearance of nesprin-2G near the mitochondria. Moreover, GFP-nesprin-2 redistribution is associated with reduction in mitochondrial membrane potential and mitochondrial outer membrane permeabilization and precedes the appearance of morphological features of apoptosis. Our results show that nesprin-2G redistribution and translocation near mitochondria is an early apoptotic effect associated with mitochondrial dysfunction, which may be responsible for the pro-apoptotic function of nesprin-2. [ABSTRACT FROM AUTHOR]

Cellular behavior is continuously influenced by mechanical forces. These forces span the cytoskeleton and reach the nucleus, where they trigger mechanotransduction pathways that regulate downstream biochemical events. Therefore, the nucleus has emerged as a regulator of cellular response to mechanical stimuli. Cell cycle progression is regulated by cyclin-CDK complexes. Recent studies demonstrated these biochemical pathways are influenced by mechanical signals, highlighting the interdependence of cellular mechanics and cell cycle regulation. In particular, the transition from G2 to mitosis (G2-M) shows significant changes in nuclear structure and organization, ranging from nuclear pore complex (NPC) and nuclear lamina disassembly to chromosome condensation. The remodeling of these mechanically active nuclear components indicates that mitotic entry is particularly sensitive to forces. Here, we address how mechanical forces crosstalk with the nucleus to determine the timing and efficiency of the G2-M transition. Finally, we discuss how the deregulation of nuclear mechanics has consequences for mitosis. [ABSTRACT FROM AUTHOR]

The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution. [ABSTRACT FROM AUTHOR]

DNA sequencing is not enough to grasp the complexity of genome organization and function. The four-dimensional (three in space, one in time) configuration of the eukaryotic nucleus varies with cell types, during development and in diseased tissues, and has to be taken into account to decipher genome function. To study, discuss, and advance in such direction, the International Nucleome Consortium COST Action, funded by the European Union, held its concluding symposium 'The Genome in Space and Time' at the Ionian University in Corfu, Greece, on September 10–13, 2023. [ABSTRACT FROM AUTHOR]

Triploids play an important role in the polyploidization process and are considered a bridge between diploids and polyploids. To inform plant polyploidization research and polyploid breeding, it is important to explore chromosome behaviour during triploid pollen development, pollen fertility problems in triploids and the potential value of utilizing triploids. In this study, acetocarmine, carbol fuchsin and fluorescence staining methods were used to observe microsporogenesis and microspore development in fertile triploid Chinese chives. The results revealed that some of the pollen mother cells were able to undergo equal chromosome distributions (approximately 36%), whereas other pollen mother cells formed lagging chromosomes, chromosome bridges, micronuclei and early cytoplasmic divisions during microsporogenesis, resulting in microspores of different sizes. Regardless of whether an equal tetrad or an abnormal polyad was formed, microspores were released from callose in a normal manner and contained nuclei. During the process of microspore development, most of the microspore nuclei disappeared gradually and ultimately formed empty pollen cells that lacked nuclei. During the meiosis of pollen mother cells in triploid Chinese chives, a variety of chromosome distribution behaviours contribute to the formation of some viable pollen. [ABSTRACT FROM AUTHOR]

Ciliates are eukaryotic unicellular organisms with complex morphology and developmental processes, including asexual and sexual processes. Conjugation is a form of sexual process that renews genetic materials. However, visualizing conjugation in ciliates is a challenge due to the complexity and dynamics of the process, while traditional staining methods are often insufficient for the research. This study introduces a new method for visualizing developmental progression in the nuclei during conjugation using Hoechst33342 staining. It describes how to proceed from cell culture, conjugation induction and synchronization, staining preparation, and observation to statistical analysis. The combination of fluorescent staining with the 'volume-fixing' technique eliminates the fixation and dehydration steps, thus reducing the overall operation time to just 20 minutes. This method offers several advantages over traditional staining techniques for studying the nuclei during conjugation. It improves image quality and workflow efficiency and enables real-time observation of live cell states. Potential solutions to challenges that may arise during experimental procedures are introduced and references and guidelines for cytological research are provided in this paper. [ABSTRACT FROM AUTHOR]

Cell cycle regulation is crucial to assure expansion of a cell population, while preserving genome integrity. This notion is especially relevant to fertilization and early embryo development, a time when the cell cycle transforms from meiotic into mitotic cycles. Zygote-to-embryo transition is acutely error-prone, causing major developmental perturbations, including cleavage delays, tri- and multi-chotomous cleavages, and cell fragmentation. Another such alteration is bi- and multinucleation, consisting of the simultaneous formation of two or more nuclei at interphase. Indeed, multinucleation affects a large proportion of early human embryos, typically at the two-cell stage. Mechanistically, several factors, including spindle dysfunction, failed cleavage, and cell fusion, may generate this cell anomaly. In assisted reproduction treatment, multinucleation is associated with reduced developmental rates and lower implantation rates in Days 2–3 embryo transfers. However, many multinucleated embryos can develop to the blastocyst stage. In blastocyst transfers, the current evidence does not suggest a major impact of a previous history of multinucleation on the odds of euploidy or successful treatment outcomes. Human embryo multinucleation remains a not-fully-understood but developmentally relevant and intriguing phenomenon which requires further research of its generative mechanisms and clinical implications. [ABSTRACT FROM AUTHOR]

One of the first cellular locations of the calreticulin (CRT) chaperone in eukaryotic cells, apart from its obvious localization in the endoplasmic reticulum (ER), was the cell nucleus (Opas et al. 1991). The presence of CRT has been detected inside the nucleus and in the nuclear envelope of animal and plant cells, and a putative nuclear localization signal (NLS) in the CRT amino acid sequence has been mapped in several animal and plant species. Over the last 30 years, other localization sites of this protein outside the ER and cell nucleus have also been discovered, suggesting that CRT is a multifunctional Ca2+-binding protein widely found in various cell types. In our previous studies focusing on plant developmental biology, we have demonstrated the presence of CRT inside and outside the ER in highly specialized plant cells, as well as the possibility of CRT localization in the cell nucleus. In this paper, we present a detailed analysis of immunocytochemical localization of CRT inside nuclei of the pistil transmission tract somatic cells before and after pollination. We show a similar pattern of the nuclear CRT localization in relation to exchangeable Ca2+ for two selected species of angiosperms, dicotyledonous Petunia and monocot Haemanthus, that differ in anatomical structure of the pistil and discuss the potential role of CRT in the cell nucleus. [ABSTRACT FROM AUTHOR]

In eukaryotic cell nuclei, specific sets of proteins gather in nuclear bodies and facilitate distinct genomic processes. The nucleolus, a nuclear body, functions as a factory for ribosome biogenesis by accumulating constitutive proteins, such as RNA polymerase I and nucleophosmin 1 (NPM1). Although in vitro assays have suggested the importance of liquid--liquid phase separation (LLPS) of constitutive proteins in nucleolar formation, how the nucleolus is structurally maintained with the intranuclear architecture remains unknown. This study revealed that the nucleolus is encapsulated by a single-stranded (ss)DNA-based molecular complex inside the cell nucleus. Super-resolution lattice-structured illumination microscopy (lattice-SIM) showed that there was a high abundance of ssDNA beyond the 'outer shell' of the nucleolus. Nucleolar disruption and the release of NPM1 were caused by in situ digestion of ssDNA, suggesting that ssDNA has a structural role in nucleolar encapsulation. Furthermore, we identified that ssDNA forms a molecular complex with histone H1 for nucleolar encapsulation. Thus, this study illustrates how an ssDNA-based molecular complex upholds the structural integrity of nuclear bodies to coordinate genomic processes such as gene transcription and replication. [ABSTRACT FROM AUTHOR]

Glyoxalase 2 (Glo2) is an enzyme of the glyoxalase system whose pathway parallels glycolysis and which aims to remove methylglyoxal (MGO). This study analyzed the possible additional roles of the Glo2 enzyme in breast cancer (MCF7) and non-cancer (HDF) cell lines, investigating its presence at the nuclear level and its potential involvement in cell proliferation and chemotherapy resistance. The results revealed that Glo2 is overexpressed in cancer cells, and its expression is higher during the proliferative (S and G2/M) phases of the cell cycle. The study also examined a post-translational modification (PTM) in which Glo2 could be involved, with S-glutathionylation revealing that Glo2 enhances this PTM in cancer cells both in the cytoplasm and nucleus. Inhibition of Glo2 by p-NCBG resulted in increased sensitivity to doxorubicin, a common chemotherapeutic agent. This suggests that Glo2 increases cancer cell resistance to chemotherapy, potentially through its role in regulating oxidative stress. These results highlight Glo2 as a potential therapeutic target to improve the efficacy of existing treatments. [ABSTRACT FROM AUTHOR]

Firstly, a topology is constructed by nuclei and upsets in residuated lattices and it is shown that a residuated lattice endowed with this topology becomes a topological space. Furthermore, some properties of the topological space are investigated such as compactness and connectedness. Moreover, we study continuities of all the operations with respect to the topology in a residuated lattice. Finally, the relationships are revealed between the two topologies on quotient residuated lattices. [ABSTRACT FROM AUTHOR]

Alterations in the rate and accuracy of messenger RNA (mRNA) translation are associated with aging and several neurodegenerative disorders, including Alzheimer's disease and related tauopathies. We previously reported that error‐containing RNA that are normally cleared via nonsense‐mediated mRNA decay (NMD), a key RNA surveillance mechanism, are translated in the adult brain of a Drosophila model of tauopathy. In the current study, we find that newly‐synthesized peptides and translation machinery accumulate within nuclear envelope invaginations that occur as a consequence of tau pathology, and that the rate of mRNA translation is globally elevated in early stages of disease in adult brains of Drosophila models of tauopathy. Polysome profiling from adult heads of tau transgenic Drosophila reveals the preferential translation of specific mRNA that have been previously linked to neurodegeneration. Unexpectedly, we find that panneuronal elevation of NMD further elevates the global translation rate in tau transgenic Drosophila, as does treatment with rapamycin. As NMD activation and rapamycin both suppress tau‐induced neurodegeneration, their shared effect on translation suggests that elevated rates of mRNA translation are an early adaptive mechanism to limit neurodegeneration. Our work provides compelling evidence that tau‐induced deficits in NMD reshape the tau translatome by increasing translation of RNA that are normally repressed in healthy cells. [ABSTRACT FROM AUTHOR]

The nucleus is a key cell mechanosensor of the local microenvironment. Nondestructive nuclear mechanosensation responses in confinement involve the build-up of the nuclear lamina, nuclear pore complex stretching-dependent exchange of nuclear–cytoplasmic constituents, and nuclear pressurization. Destructive nuclear mechanoresponses include the nuclear depletion of DNA repair factors and nuclear influx of TREX1 exonuclease, which promote DNA damage, as well as the cytoplasmic access of double-strand (ds)DNA, which can trigger a cyclic GMP-AMP synthase pathway/stimulator of interferon genes (cGAS/STING) response. Ion channels are among the first molecules to sense and respond to different physical stimuli, including confinement, by regulating intracellular ionic concentrations and water fluxes, thereby altering cell motility. The crosstalk between nuclear mechanotransduction and ion channel-mediated signaling enables efficient cell migration through confining spaces. Cell surface and intracellular mechanosensors enable cells to perceive different geometric, topographical, and physical cues. Mechanosensitive ion channels (MICs) localized at the cell surface and on the nuclear envelope (NE) are among the first to sense and transduce these signals. Beyond compartmentalizing the genome of the cell and its transcription, the nucleus also serves as a mechanical gauge of different physical and topographical features of the tissue microenvironment. In this review, we delve into the intricate mechanisms by which the nucleus and different ion channels regulate cell migration in confinement. We review evidence suggesting an interplay between macromolecular nuclear–cytoplasmic transport (NCT) and ionic transport across the cell membrane during confined migration. We also discuss the roles of the nucleus and ion channel-mediated mechanosensation, whether acting independently or in tandem, in orchestrating migratory mechanoresponses. Understanding nuclear and ion channel sensing, and their crosstalk, is critical to advancing our knowledge of cell migration in health and disease. [ABSTRACT FROM AUTHOR]

We offer here a particularly simple and direct construction of the congruence frame of a given frame, aka its assembly, from the bounded meet semilattice of differences of frame elements. The construction enables economical proofs of two of the assembly's known attributes, namely ultranormality and ultraparacompactness, as well as a proof that the assembly is an essential extension of the frame with the same essential closure as the frame. The major new result is that the assembly is free over its meet semilattice of differences. [ABSTRACT FROM AUTHOR]

Recent work by Busaniche, Galatos and Marcos introduced a very general twist construction, based on the notion of conucleus, which subsumes most existing approaches. In the present paper we extend this framework one step further, so as to allow us to construct and represent algebras which possess a negation that is not necessarily involutive. Our aim is to capture the main properties of the largest class that admits such a representation, as well as to be able to recover the well-known cases—such as (quasi-)Nelson algebras and (quasi-)N4-lattices—as particular instances of the general construction. We pursue two approaches, one that directly generalizes the classical Rasiowa construction for Nelson algebras, and an alternative one that allows us to study twist-algebras within the theory of residuated lattices. [ABSTRACT FROM AUTHOR]

Mechanical vibration has been shown to regulate cell proliferation and differentiation in vitro and in vivo. However, the mechanism of its cellular mechanotransduction remains unclear. Although the measurement of intracellular deformation dynamics under mechanical vibration could reveal more detailed mechanisms, corroborating experimental evidence is lacking due to technical difficulties. In this study, we aimed to propose a real‐time imaging method of intracellular structure deformation dynamics in vibrated adherent cell cultures and investigate whether organelles such as actin filaments connected to a nucleus and the nucleus itself show deformation under horizontal mechanical vibration. The proposed real‐time imaging was achieved by conducting vibration isolation and making design improvements to the experimental setup; using a high‐speed and high‐sensitivity camera with a global shutter; and reducing image blur using a stroboscope technique. Using our system, we successfully produced the first experimental report on the existence of the deformation of organelles connected to a nucleus and the nucleus itself under horizontal mechanical vibration. Furthermore, the intracellular deformation difference between HeLa and MC3T3‐E1 cells measured under horizontal mechanical vibration agrees with the prediction of their intracellular structure based on the mechanical vibration theory. These results provide new findings about the cellular mechanotransduction mechanism under mechanical vibration. [ABSTRACT FROM AUTHOR]

The proximal tubule (PT) is a nephron segment that is responsible for the majority of solute and water reabsorption in the kidney. Each of its sub-segments have specialized functions; however, little is known about the genes and proteins that determine the oxidative phosphorylation capacity of the PT sub-segments. This information is critical to understanding kidney function and will provide a comprehensive landscape of renal cell adaptations to injury, physiologic stressors, and development. This study analyzed three immortalized murine renal cell lines (PT S1, S2, and S3 segments) for protein content and compared them to a murine fibroblast cell line. All three proximal tubule cell lines generate ATP predominantly by oxidative phosphorylation while the fibroblast cell line is glycolytic. The proteomic data demonstrates that the most significant difference in proteomic signatures between the cell lines are proteins known to be localized in the nucleus followed by mitochondrial proteins. Mitochondrial metabolic substrate utilization assays were performed using the proximal tubule cell lines to determine substrate utilization kinetics thereby providing a physiologic context to the proteomic dataset. This data will allow researchers to study differences in nephron-specific cell lines, between epithelial and fibroblast cells, and between actively respiring cells and glycolytic cells. SIGNIFICANCE: Proteomic analysis of proteins expressed in immortalized murine renal proximal tubule cells was compared to a murine fibroblast cell line proteome. The proximal tubule segment specific cell lines: S1, S2 and S3 are all grown under conditions whereby the cells generate ATP by oxidative phosphorylation while the fibroblast cell line utilizes anaerobic glycolysis for ATP generation. The proteomic studies allow for the following queries: 1) comparisons between the proximal tubule segment specific cell lines, 2) comparisons between polarized epithelia and fibroblasts, 3) comparison between cells employing oxidative phosphorylation versus anaerobic glycolysis and 4) comparisons between cells grown on clear versus opaque membrane supports. The data finds major differences in nuclear protein expression and mitochondrial proteins. This proteomic data set will be an important baseline dataset for investigators who need immortalized renal proximal tubule epithelial cells for their research.

Abstract This study focuses on developing machine learning models to detect subtle alterations in hepatocyte chromatin organization due to Iron (II, III) oxide nanoparticle exposure, hypothesizing that exposure will significantly alter chromatin texture. A total of 2000 hepatocyte nuclear regions of interest (ROIs) from mouse liver tissue were analyzed, and for each ROI, 5 different parameters were calculated: Long Run Emphasis, Short Run Emphasis, Run Length Nonuniformity, and 2 wavelet coefficient energies obtained after the discrete wavelet transform. These parameters served as input for supervised machine learning models, specifically random forest and gradient boosting classifiers. The models demonstrated relatively robust performance in distinguishing hepatocyte chromatin structures belonging to the group exposed to IONPs from the controls. The study's findings suggest that iron oxide nanoparticles induce substantial changes in hepatocyte chromatin distribution and underscore the potential of AI techniques in advancing hepatocyte evaluation in physiological and pathological conditions.

Abstract Heat stress (HS) impacts the nuclear proteome and, subsequently, protein activities in different nuclear compartments. In Arabidopsis thaliana, a short exposure to 37 °C leads to loss of the standard tripartite architecture of the nucleolus, the most prominent nuclear substructure, and, consequently, affects the assembly of ribosomes. Here, we report a quantitative label-free LC‒MS/MS (Liquid Chromatography coupled to tandem Mass Spectrometry) analysis to determine the nuclear proteome of Arabidopsis at 22 °C, HS (37 °C for 4 and 24 h), and a recovery phase. This analysis identified ten distinct groups of proteins based on relative abundance changes in the nucleus before, during and after HS: Early, Late, Transient, Early Persistent, Late Persistent, Recovery, Early-Like, Late-Like, Transient-Like and Continuous Groups (EG, LG, TG, EPG, LPG, RG, ELG, LLG, TLG and CG, respectively). Interestingly, the RNA polymerase I subunit NRPA3 and other main nucleolar proteins, including NUCLEOLIN 1 and FIBRILLARIN 1 and 2, were detected in RG and CG, suggesting that plants require increased nucleolar activity and likely ribosome assembly to restore protein synthesis after HS.

Freshman general science students already know that the atom is composed of a nucleus containing protons and neutrons with electrons circling the nucleus. This hands-on modeling lab allows students to visualize and discover the that electrons' mass is far less and negligible compared to the nucleus. They probably have been taught this in previous science classes through memorization. [ABSTRACT FROM AUTHOR]

3D cell culture has emerged as a promising approach to replicate the complex behaviors of cells within living organisms. This study aims to analyze spatiotemporal behavior of the morphological characteristics of cell structure at multiscale in 3D scaffold-free spheroids using chondrogenic progenitor ATDC5 cells. Over a 14-day culture period, it exhibited cell hypertrophy in the spheroids regarding cellular and nuclear size as well as changes in morphology. Moreover, biological analysis indicated a signification up-regulation of normal chondrocyte as well as hypertrophic chondrocyte markers, suggesting early hypertrophic chondrocyte differentiation. Cell nuclei underwent changes in volume, sphericity, and distribution in spheroid over time, indicating alterations in chromatin organization. The ratio of chromatin condensation volume to cell nuclear volume decreased as the cell nuclei enlarged, potentially signifying changes in chromatin state during hypertrophic chondrocyte differentiation. Our image analysis techniques in this present study enabled detailed morphological measurement of cell structure at multi-scale, which can be applied to various 3D culture models for in-depth investigation. [ABSTRACT FROM AUTHOR]

This study focuses on developing machine learning models to detect subtle alterations in hepatocyte chromatin organization due to Iron (II, III) oxide nanoparticle exposure, hypothesizing that exposure will significantly alter chromatin texture. A total of 2000 hepatocyte nuclear regions of interest (ROIs) from mouse liver tissue were analyzed, and for each ROI, 5 different parameters were calculated: Long Run Emphasis, Short Run Emphasis, Run Length Nonuniformity, and 2 wavelet coefficient energies obtained after the discrete wavelet transform. These parameters served as input for supervised machine learning models, specifically random forest and gradient boosting classifiers. The models demonstrated relatively robust performance in distinguishing hepatocyte chromatin structures belonging to the group exposed to IONPs from the controls. The study's findings suggest that iron oxide nanoparticles induce substantial changes in hepatocyte chromatin distribution and underscore the potential of AI techniques in advancing hepatocyte evaluation in physiological and pathological conditions. [ABSTRACT FROM AUTHOR]

Lamins are intermediate filament proteins that contribute to numerous cellular functions, including nuclear morphology and mechanical stability. The N-terminal head domain of lamin is crucial for higher order filament assembly and function, yet the effects of commonly used N-terminal tags on lamin function remain largely unexplored. Here, we systematically studied the effect of two differently sized tags on lamin A (LaA) function in a mammalian cell model engineered to allow for precise control of expression of tagged lamin proteins. Untagged, FLAG-tagged and GFP-tagged LaA completely rescued nuclear shape defects when expressed at similar levels in lamin A/C-deficient (Lmna-/-) MEFs, and all LaA constructs prevented increased nuclear envelope ruptures in these cells. N-terminal tags, however, altered the nuclear localization of LaA and impaired the ability of LaA to restore nuclear deformability and to recruit emerin to the nuclear membrane in Lmna-/- MEFs. Our finding that tags impede some LaA functions but not others might explain the partial loss of function phenotypes when tagged lamins are expressed in model organisms and should caution researchers using tagged lamins to study the nucleus. [ABSTRACT FROM AUTHOR]

Heat stress (HS) impacts the nuclear proteome and, subsequently, protein activities in different nuclear compartments. In Arabidopsis thaliana, a short exposure to 37 °C leads to loss of the standard tripartite architecture of the nucleolus, the most prominent nuclear substructure, and, consequently, affects the assembly of ribosomes. Here, we report a quantitative label-free LC‒MS/MS (Liquid Chromatography coupled to tandem Mass Spectrometry) analysis to determine the nuclear proteome of Arabidopsis at 22 °C, HS (37 °C for 4 and 24 h), and a recovery phase. This analysis identified ten distinct groups of proteins based on relative abundance changes in the nucleus before, during and after HS: Early, Late, Transient, Early Persistent, Late Persistent, Recovery, Early-Like, Late-Like, Transient-Like and Continuous Groups (EG, LG, TG, EPG, LPG, RG, ELG, LLG, TLG and CG, respectively). Interestingly, the RNA polymerase I subunit NRPA3 and other main nucleolar proteins, including NUCLEOLIN 1 and FIBRILLARIN 1 and 2, were detected in RG and CG, suggesting that plants require increased nucleolar activity and likely ribosome assembly to restore protein synthesis after HS. [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]

We develop a hierarchy of semilattice bases (S-bases) for frames. For a given (unbounded) meet-semilattice A, we analyze the interval in the coframe of sublocales of the frame of downsets of A formed by all frames with the S-base A. We study various degrees of completeness of A, which generalize the concepts of extremally disconnected and basically disconnected frames. We introduce the concepts of D-bases and L-bases, as well as their bounded counterparts, and show how our results specialize and sharpen in these cases. Classic examples that are covered by our approach include zero-dimensional, completely regular, and coherent frames, allowing us to provide a new perspective on these well-studied classes of frames, as well as their spatial counterparts. [ABSTRACT FROM AUTHOR]

Cholesterol is required to maintain the functional integrity of cellular membrane systems and signalling pathways, but its supply must be closely and dynamically regulated because excess cholesterol is toxic. Sterol regulatory element-binding protein 2 (SREBP2) and the ER-resident protein HMG-CoA reductase (HMGCR) are key regulators of cholesterol biosynthesis. Here, we assessed the mechanistic aspects of their regulation in hepatic cells. Unexpectedly, we found that the transcriptionally active fragment of SREBP2 (N-SREBP2) was produced constitutively. Moreover, in the absence of an exogenous cholesterol supply, nuclear N-SREBP2 became resistant to proteasome-mediated degradation. This resistance was paired with increased occupancy at the HMGCR promoter and HMGCR expression. Inhibiting nuclear N-SREBP2 degradation did not increase HMGCR RNA levels; this increase required cholesterol depletion. Our findings, combined with previous physiological and biophysical investigations, suggest a new model of SREBP2-mediated regulation of cholesterol biosynthesis in the organ that handles large and rapid fluctuations in the dietary supply of this key lipid. Specifically, in the nucleus, cholesterol and the ubiquitin–proteasome system provide a short-loop system that modulates the rate of cholesterol biosynthesis via regulation of nuclear N-SREBP2 turnover and HMGCR expression. Our findings have important implications for maintaining cellular cholesterol homeostasis and lowering blood cholesterol via the SREBP2-HMGCR axis. [ABSTRACT FROM AUTHOR]

Cells are capable of sensing and responding to the extracellular mechanical microenvironment via the actin skeleton. In vivo, tissues are frequently subject to mechanical forces, such as the rapid and significant shear flow encountered by vascular endothelial cells. However, the investigations about the transient response of intracellular actin networks under these intense external mechanical forces, their intrinsic mechanisms, and potential implications are very limited. Here, we observe that when cells are subject to the shear flow, an actin ring structure could be rapidly assembled at the periphery of the nucleus. To gain insights into the mechanism underlying this perinuclear actin ring assembly, we develop a computational model of actin dynamics. We demonstrate that this perinuclear actin ring assembly is triggered by the depolymerization of cortical actin, Arp2/3-dependent actin filament polymerization, and myosin-mediated actin network contraction. Furthermore, we discover that the compressive stress generated by the perinuclear actin ring could lead to a reduction in the nuclear spreading area, an increase in the nuclear height, and a decrease in the nuclear volume. The present model thus explains the mechanism of the perinuclear actin ring assembly under external mechanical forces and suggests that the spontaneous contraction of this actin structure can significantly impact nuclear morphology. [ABSTRACT FROM AUTHOR]

It is well-known that the Dedekind-MacNeille completion of a poset is its injective hull. We prove that the injective hull of an ordered universal algebra with respect to a specific class of monomorphisms has properties that are similar to the properties of the Dedekind-MacNeille completion of a poset. In particular, this injective hull induces a reflector functor from the category of ordered algebras and continuous morphisms to the category of sup-algebras. [ABSTRACT FROM AUTHOR]

Correctly measuring of the moments of inertia of fragments of binary fission of actinide nuclei helps solve the important problem in nuclear physics of determining the spins of such fragments. The moments of inertia are calculated using the solid rotation, hydrodynamic, and superfluid models. The best agreement with experimental data is obtained using the superfluid model with an oscillatory potential. [ABSTRACT FROM AUTHOR]

This paper deals with substructural nuclear (image-based) logics and their algebraic and Kripke-style semantics. More precisely, we first introduce a class of substructural logics with connective N satisfying nucleus property, called here substructural nuclear logics, and its subclass, called here substructural nuclear image-based logics, where N further satisfies homomorphic image property. We then consider their algebraic semantics together with algebraic characterizations of those logics. Finally, we introduce operational Kripke-style semantics for those logics and provide two sorts of completeness results for them, one of which is based on algebraic completeness for all the logics and the other of which is based on set-theoretic one for the nuclear image-based logics. [ABSTRACT FROM AUTHOR]

Purpose: This study evaluated whether a nanostructured lipid carrier (NLC) delivery system could safely and accurately deliver nucleic acids to the cell nucleus using the enhanced green fluorescent protein (EGFP)-C1 plasmid model. Methods: The NLC was formulated using the emulsification method and equipped for cationic lipid-mediated transfection with 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), which interacts electrostatically with nucleic acid. The NLC attributes, including size, polydispersity index, and zeta potential, were assessed by dynamic light scattering (DLS). The morphological structure was analyzed using transmission electron microscopy. Entrapment efficiency was evaluated by a direct method. Cellular uptake mechanisms of pEGFP-C1-NLC and the ability of pEGFP-C1 to penetrate the nucleus of TM4 cells to express EGFP were observed using confocal microscopy. Results: pEGFP-C1-NLC exhibited particle sizes in the range 56-88 nm with a particle charge range of -6.0 to+1.3 mV. The polydispersity index<0.5 showed good size uniformity, and entrapment efficiency of pEGFP-C1in the NLC was 92.06±2.295%. The NLC formulation was internalized predominantly via caveolae-mediated endocytosis, as indicated by EGFP expression following successful delivery of pEGFP by the NLC into the cells. Conclusion: NLC formulation could deliver genetic material to the nucleus and could be considered a gene therapy candidate for spermatogenesis. [ABSTRACT FROM AUTHOR]

Cryptococcus neoformans is a fungal pathogen of the top critical priority recognized by the World Health Organization. This clinically important fungus also serves as a eukaryotic model organism. A variety of resources have been generated to facilitate investigation of the C. neoformans species complex, including congenic pairs, well-annotated genomes, genetic editing tools, and gene deletion sets. Here, we generated a set of strains with all major organelles fluorescently marked. We tested short organelle-specific targeting sequences and successfully labeled the following organelles by fusing the targeting sequences with a fluorescence protein: the plasma membrane, the nucleus, the peroxisome, and the mitochondrion. We used native cryptococcal Golgi and late endosomal proteins fused with a fluorescent protein to label these two organelles. These fluorescence markers were verified via colocalization using organelle-specific dyes. All the constructs for the fluorescent protein tags were integrated in an intergenic safe haven region. These organelle-marked strains were examined for growth and various phenotypes. We demonstrated that these tagged strains could be employed to track cryptococcal interaction with the host in phagocytosis assays. These strains also allowed us to discover remarkable differences in the dynamics of proteins targeted to different organelles during sexual reproduction. Additionally, we revealed that "dormant" spores transcribed and synthesized their own proteins and trafficked the proteins to the appropriate subcellular compartments, demonstrating that spores are metabolically active. We anticipate that these newly generated fluorescent markers will greatly facilitate further investigation of cryptococcal biology and pathogenesis. [ABSTRACT FROM AUTHOR]

Mitosis is an essential process in which the duplicated genome is segregated equally into two daughter cells. CTCF has been reported to be present in mitosis and has a role in localizing CENP-E, but its importance for mitotic fidelity remains to be determined. To evaluate the importance of CTCF in mitosis, we tracked mitotic behaviors in wild-type and two different CTCF CRISPR-based genetic knockdowns. We find that knockdown of CTCF results in prolonged mitoses and failed anaphase segregation via time-lapse imaging of SiR-DNA. CTCF knockdown did not alter cell cycling or the mitotic checkpoint, which was activated upon nocodazole treatment. Immunofluorescence imaging of the mitotic spindle in CTCF knockdowns revealed disorganization via tri/tetrapolar spindles and chromosomes behind the spindle pole. Imaging of interphase nuclei showed that nuclear size increased drastically, consistent with failure to divide the duplicated genome in anaphase. Long-term inhibition of CNEP-E via GSK923295 recapitulates CTCF knockdown abnormal mitotic spindles with polar chromosomes and increased nuclear sizes. Population measurements of nuclear shape in CTCF knockdowns do not display decreased circularity or increased nuclear blebbing relative to wild-type. However, failed mitoses do display abnormal nuclear morphologies relative to successful mitoses, suggesting that population images do not capture individual behaviors. Thus, CTCF is important for both proper metaphase organization and anaphase segregation which impacts the size and shape of the interphase nucleus likely through its known role in recruiting CENP-E. [ABSTRACT FROM AUTHOR]

A 14-year boy is given a microscope by his parents. It is not a toy – but a real microscope. He deploys it to rediscover the biology he had known before, but now in a magnified world. With extraordinary intellectual gifts he then, and manifestly later becomes absorbed by the idea that all this, however mysterious at first glance, might be subject to rational understanding, with painstaking study. Thus, was the genesis of one of the greatest cell biologists of the 20th century, Joseph Grafton Gall, who died 12 September 2024, at 96. He had been professionally active up until only a few years ago. There was no one like him in the modern era of cell biology and there will not be another figure like him anytime soon.

Accumulating evidence suggests that the nuclear envelope (NE) is not just a target, but also a mediator of apoptosis. We showed recently that the NE protein nesprin-2 has pro-apoptotic activity, which involves its subcellular redistribution and Bcl-2 proteins. Here we further characterize the pro-apoptotic activity of nesprin-2 focusing on its redistribution. We assessed the redistribution kinetics of endogenous nesprin-2 tagged with GFP relative to apoptosis-associated mitochondrial dysfunction. The results show apoptosis-induced GFP-nesprin-2G redistribution occurred by two different modes – complete and partial, both lead to appearance of nesprin-2G near the mitochondria. Moreover, GFP-nesprin-2 redistribution is associated with reduction in mitochondrial membrane potential and mitochondrial outer membrane permeabilization and precedes the appearance of morphological features of apoptosis. Our results show that nesprin-2G redistribution and translocation near mitochondria is an early apoptotic effect associated with mitochondrial dysfunction, which may be responsible for the pro-apoptotic function of nesprin-2.

Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.

The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.

DNA sequencing is not enough to grasp the complexity of genome organization and function. The four-dimensional (three in space, one in time) configuration of the eukaryotic nucleus varies with cell types, during development and in diseased tissues, and has to be taken into account to decipher genome function. To study, discuss, and advance in such direction, the International Nucleome Consortium COST Action, funded by the European Union, held its concluding symposium ‘The Genome in Space and Time’ at the Ionian University in Corfu, Greece, on September 10–13, 2023.

The members of the evolutionary conserved actin-binding Ezrin, Radixin and Moesin (ERM) protein family are involved in numerous key cellular processes in the cytoplasm. In the last decades, ERM proteins, like actin and other cytoskeletal components, have also been shown to be functional components of the nucleus; however, the molecular mechanism behind their nuclear activities remained unclear. Therefore, our primary aim was to identify the nuclear protein interactome of the single Drosophila ERM protein, Moesin. We demonstrate that Moesin directly interacts with the Mediator complex through direct binding to its Med15 subunit, and the presence of Moesin at the regulatory regions of the Hsp70Ab heat shock gene was found to be Med15-dependent. Both Moesin and Med15 bind to heat shock factor (Hsf), and they are required for proper Hsp gene expression under physiological conditions. Moreover, we confirmed that Moesin, Med15 and Hsf are able to bind the monomeric form of actin and together they form a complex in the nucleus. These results elucidate a mechanism by which ERMs function within the nucleus. Finally, we present the direct interaction of the human orthologues of Drosophila Moesin and Med15, which highlights the evolutionary significance of our finding.

The endosymbiotic theory posits that ancient eukaryotic cells engulfed O2-consuming prokaryotes, which protected them against O2 toxicity. Previous studies have shown that cells lacking cytochrome c oxidase (COX), required for respiration, have increased DNA damage and reduced proliferation, which could be improved by reducing O2 exposure. With recently developed fluorescence lifetime microscopy-based probes demonstrating that the mitochondrion has lower [O2] than the cytosol, we hypothesized that the perinuclear distribution of mitochondria in cells may create a barrier for O2 to access the nuclear core, potentially affecting cellular physiology and maintaining genomic integrity. To test this hypothesis, we utilized myoglobin-mCherry fluorescence lifetime microscopy O2 sensors without subcellular targeting (cytosol) or with targeting to the mitochondrion or nucleus for measuring their localized O2 homeostasis. Our results showed that, similar to the mitochondria, the nuclear [O2] was reduced by ∼20 to 40% compared with the cytosol under imposed O2 levels of ∼0.5 to 18.6%. Pharmacologically inhibiting respiration increased nuclear O2 levels, and reconstituting O2 consumption by COX reversed this increase. Similarly, genetic disruption of respiration by deleting SCO2, a gene essential for COX assembly, or restoring COX activity in SCO2-/- cells by transducing with SCO2 cDNA replicated these changes in nuclear O2 levels. The results were further supported by the expression of genes known to be affected by cellular O2 availability. Our study reveals the potential for dynamic regulation of nuclear O2 levels by mitochondrial respiratory activity, which in turn could affect oxidative stress and cellular processes such as neurodegeneration and aging.

Mechanosignaling describes processes by which biomechanical stimuli are transduced into cellular responses. External biophysical forces can be transmitted via structural protein networks that span from the cellular membrane to the cytoskeleton and the nucleus, where they can regulate gene expression through a series of biomechanical and/or biochemical mechanosensitive mechanisms, including chromatin remodeling, translocation of transcriptional regulators, and epigenetic factors. Striated muscle cells, including cardiac and skeletal muscle myocytes, utilize these nuclear mechanosignaling mechanisms to respond to changes in their intracellular and extracellular mechanical environment and mediate gene expression and cell remodeling. In this brief review, we highlight and discuss recent experimental work focused on the pathway of biomechanical stimulus propagation at the nucleus-cytoskeleton interface of striated muscles, and the mechanisms by which these pathways regulate gene regulation, muscle structure, and function. Furthermore, we discuss nuclear protein mutations that affect mechanosignaling function in human and animal models of cardiomyopathy. Furthermore, current open questions and future challenges in investigating striated muscle nuclear mechanosignaling are further discussed.

As cells migrate through biological tissues, they must frequently squeeze through micron-sized constrictions in the form of interstitial pores between extracellular matrix fibers and/or other cells. Although it is now well recognized that such confined migration is limited by the nucleus, which is the largest and stiffest organelle, it remains incompletely understood how cells apply sufficient force to move their nucleus through small constrictions. Here, we report a mechanism by which contraction of the cell rear cortex pushes the nucleus forward to mediate nuclear transit through constrictions. Laser ablation of the rear cortex reveals that pushing forces behind the nucleus are the result of increased intracellular pressure in the rear compartment of the cell. The pushing forces behind the nucleus depend on accumulation of actomyosin in the rear cortex and require Rho kinase (ROCK) activity. Collectively, our results suggest a mechanism by which cells generate elevated intracellular pressure in the posterior compartment to facilitate nuclear transit through threedimensional (3D) constrictions. This mechanism might supplement or even substitute for other mechanisms supporting nuclear transit, ensuring robust cell migrations in confined 3D environments. [ABSTRACT FROM AUTHOR]