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Mathematical methods of analysis of the spatial and ontogenetic structure of rare plant species cenopopulations allow us to reveal organization features of individual plant populations and phytocenoses as a whole. The authors study the features of the Stipa korshinskyi Roshev. (Poaceae) population structure in the Samara High Trans-Volga Region (Sernovodny Shihan, Sergievsky District, Samara Region). Spatial location and age conditions of individuals are determined according to traditional population-ontogenetic methods. The characteristics of the distribution of individuals of S. korshinskyi , taking into account their age, are determined using modern mathematical methods. With the help of the nuclear function, it was revealed that the density of the feather grass individuals in the described cenopopulation varied in the range of 1-3 individuals per 1 m. Analysis of S. korshinskyi individuals location intensity in coenopulation using the square method showed the presence of compacted and rarefied sections. The graphical interpretation of the Ripley function showed that in the studied cenopopulation the plants are randomly distributed. Using the distribution map of the dominant age states it was noted that the generative plants were closer to the periphery of the site. Graphic interpretation of Ripleys cross-function showed that young and mature plants are placed randomly in cenopopulation. Apparently, on the whole, the random nature of the individuals distribution is characteristic of S. korshinskyi cenopopulations experiencing a significant anthropogenic load in the composition of the phytocenoses.

Fasciculation and elongation zeta-1 (FEZ1) protein is involved in axon outgrowth and is highly expressed in the brain. It has multiple interaction partners, with functions varying from the regulation of neuronal development and intracellular transport mechanisms to transcription regulation. One of its interactors is retinoic acid receptor (RAR), which is activated by retinoic acid and controls many target genes and physiological process. Based on previous evidence suggesting a possible nuclear role for FEZ1, we wanted to deepen our understanding of this function by addressing the FEZ1-RAR interaction. We performed in vitro binding experiments and assessed the interface of interaction between both proteins. We found that FEZ1-RAR interacted with a similar magnitude as RAR to its responsive element DR5 and that the interaction occurred in the coiled-coil region of FEZ1 and in the ligand-binding domain of RAR. Furthermore, cellular experiments were performed in order to confirm the interaction and screen for induced target genes from an 86-gene panel. The analysis of gene expression showed that only in the presence of retinoic acid did FEZ1 induce hoxb4 gene expression. This finding is consistent with data from the literature showing the hoxb4 gene functionally involved in development and acute myeloid leukemia, as is FEZ1.

Over the past two decades, it has become clear that the multiscale spatial and temporal organization of the genome has important implications for nuclear function. This review centers on insights gained from recent advances in light microscopy on our understanding of transcription. We discuss spatial and temporal aspects that shape nuclear order and their consequences on regulatory components, focusing on genomic scales most relevant to function. The emerging picture is that spatiotemporal constraints increase the complexity in transcriptional regulation, highlighting new challenges, such as uncertainty about how information travels from molecular factors through the genome and space to generate a functional output.

Triple negative breast cancer (TNBC) has poor prognosis and neither established biomarkers nor therapeutic targets. On the one hand the androgen receptor (AR), a steroid hormone receptor (SR) which is expressed in 10-53% of TNBC and proved to be critical for BC proliferation, has been proposed as a new target in TNBC. On the other hand, we and others have shown that membrane ErbB-2 migrates to the nucleus (nuclear ErbB-2, NErbB-2) where it binds DNA at HER-2 associated sequences (HAS) to regulate BC proliferation and migration. Since we have previously shown a functional interplay between growth factors and SR signaling pathways in BC, we propose the existence of an interaction between AR and ErbB-2 which is involved in NErbB-2+/AR+ BC growth. The experimental model used was the human TNBC cell line MDA-MB-453 which displays high expression levels of AR and NErbB-2. By Western Blot (WB) we found that dihydrotestosterone (DHT) treatment for short times (minutes) did not regulate ErbB-2 phosphorylation status at residues Tyr1221/1222 and 1248 which were constitutively activated. However, DHT led to an increase in ErbB-2 phosphorylation at residue Tyr877 which we have proved to be required for ErbB-2 nuclear migration. The latter effect was blocked by the AR antagonist enzalutamide (enza). Blockage of Src activity with dasatinib inhibited DHT-induced ErbB-2 phosphorylation at Tyr877. By Immunofluorescence and confocal microscopy analyses and subcellular fractionation studies we demonstrated that DHT induced ErbB-2 nuclear migration which was inhibited by enza. By chIP we found that DHT induced ErbB-2 recruitment to a HAS site in ERK5, a gene involved in BC proliferation, and to a HAS site in FKBP5, a classical AR responsive gene. By WB we demonstrated that transfection with an ErbB-2 mutant which is unable to translocate to the nucleus and functions as a dominant negative inhibitor of ErbB-2 nuclear migration (hErbB-2ΔNLS), inhibited FKBP51 up-regulation by DHT. Finally, by microarray and bioinformatics analysis we identified 315 differentially expressed genes (DEGs) in the presence of DHT and NErbB-2 eviction. Enrichment analyses showed that the DEGs belonged to the immune response and interferon pathways. Kaplan-Meier analysis revealed that the expression of 6 genes was significantly associated with overall survival in TNBC patients from the METABRIC cohort: CXCL10, TAP1, STAT1, NMI, HLA-A and NLRC5. Multivariate Cox regression analysis identified the combined expression of the 6 genes as an independent predictor of better clinical outcome in TNBC (HR: 0.56, 95% CI 0.38-0.82, P = 0.003). In conclusion, our findings evidence that DHT-activated AR induces Src-mediated ErbB-2 rapid activation and its migration to the nucleus where it binds to HAS sites in the DNA. Moreover, based on the DEGs of NErbB-2 eviction in presence of DHT we identified a gene signature associated with favorable outcome in TNBC.

In the past decade, two major advances in our understanding of nuclear organization have taken the field of gene regulation by storm. First, technologies that can analyze the three-dimensional conformation of chromatin have revealed how the genome is organized and have provided novel insights into how regulatory regions in the genome interact. Second, the recognition that many proteins can form membraneless compartments through liquid-liquid phase separation (LLPS) has challenged long-standing notions of how proteins within the nucleus are organized and has offered a tantalizing general mechanism by which many aspects of nuclear function may be regulated. However, the functional roles of chromatin topology and LLPS in regulating gene expression remain poorly understood. These topics were discussed with great fervor during an open discussion held at a recent workshop titled ‘Chromatin-based regulation of development’ organized by The Company of Biologists. Here, we summarize the major points covered during this debate and discuss how they tie into current thinking in the field of gene regulation.

Positioned at the axis between the cell and its environment, mTOR directs a wide range of cellular activity in response to nutrients, growth factors, and stress. Our understanding of the role of mTOR is evolving beyond the spatial confines of the cytosol, and its role in the nucleus becoming ever more apparent. In this review, we will address various studies that explore the role of nuclear mTOR (nmTOR) in specific cellular programs and how these pathways influence one another. To understand the emerging roles of nuclear mTOR, we discuss data and propose plausible mechanisms to offer novel ideas, hypotheses, and future research directions.

The organization of interphase chromosomes in chromosome territories (CTs) was first proposed more than one hundred years ago. The introduction of increasingly sophisticated microscopic and molecular techniques, now provide complementary strategies for studying CTs in greater depth than ever before. Here we provide an overview of these strategies and how they are being used to elucidate CT interactions and the role of these dynamically regulated, nuclear-structure building blocks in directly supporting nuclear function in a physiologically responsive manner.

Since the discovery of SUMO twenty years ago, SUMO conjugation has become a widely recognized post-translational modification that targets a myriad of proteins in many processes. Great progress has been made in understanding the SUMO pathway enzymes, substrate sumoylation, and the interplay between sumoylation and other regulatory mechanisms in a variety of contexts. As these research directions continue to generate insights into SUMO-based regulation, several mechanisms by which sumoylation and desumoylation can orchestrate large biological effects are emerging. These include the ability to target multiple proteins within the same cellular structure or process, respond dynamically to external and internal stimuli, and modulate signaling pathways involving other post-translational modifications. Focusing on nuclear function and intracellular signaling, this review highlights a broad spectrum of historical data and recent advances with the aim of providing an overview of mechanisms underlying SUMO-mediated global effects to stimulate further inquiry into intriguing roles of SUMO.

Interleukin-33 (IL-33) is the most attractive novel cytokine identified as an IL-1family member. IL-33 was first named NF-HEV (nuclear factor from high endothelial venules), as itwas known to interact with nuclear chromatin although its exact intracellular functions are still tobe clarified. IL-33 is now recognized as the specific ligand for the orphan IL-1 receptor familymember ST2 and to be involved in polarization of T cells towards T helper 2-cell phenotype and inactivation of mast cells, basophils, eosinophils and natural killer cells. It is essential for IL-33 to beextracellularly released in order to bind to the ST2 receptor and consequently play a crucial role ininflammatory, infectious and autoimmune diseases. However, like the IL-1 family members, IL-1beta and IL-18, IL-33 mRNA is translated without a signal sequence for secretion. Additionally, IL-33 cannot be released by the processing and secretion mechanism shared by IL-1beta and IL-18as IL-33 is not a substrate of caspase-1 and does not require proteolysis for activation. In contrast,IL-33 can be inactivated by apoptotic caspases. Accordingly, IL-33 is proposed to be released asan alarmin from necrotic cells but deleted during apoptosis. Besides the known autocrine,paracrine mechanisms of cellular interaction with cytokines, release by necrotic cells is anotherpathway for a cytokine to display its function, which we suggest might be called 'necrocrine'.

The finding that small non-coding RNAs (ncRNAs) are able to control gene expression in a sequence specific manner has had a massive impact on biology. Recent improvements in high throughput sequencing and computational prediction methods have allowed the discovery and classification of several types of ncRNAs. Based on their precursor structures, biogenesis pathways and modes of action, ncRNAs are classified as small interfering RNAs (siRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs), promoter associate RNAs (pRNAs), small nucleolar RNAs (snoRNAs) and sno-derived RNAs. Among these, miRNAs appear as important cytoplasmic regulators of gene expression. miRNAs act as post-transcriptional regulators of their messenger RNA (mRNA) targets via mRNA degradation and/or translational repression. However, it is becoming evident that miRNAs also have specific nuclear functions. Among these, the most studied and debated activity is the miRNA-guided transcriptional control of gene expression. Although available data detail quite precisely the effectors of this activity, the mechanisms by which miRNAs identify their gene targets to control transcription are still a matter of debate. Here, we focus on nuclear functions of miRNAs and on alternative mechanisms of target recognition, at the promoter lavel, by miRNAs in carrying out transcriptional gene silencing.

Insulator bodies are novel nuclear stress foci that can be used as a proxy to monitor the chromatin-bound state of insulator proteins., Chromatin insulators assist in the formation of higher-order chromatin structures by mediating long-range contacts between distant genomic sites. It has been suggested that insulators accomplish this task by forming dense nuclear foci termed insulator bodies that result from the coalescence of multiple protein-bound insulators. However, these structures remain poorly understood, particularly the mechanisms triggering body formation and their role in nuclear function. In this paper, we show that insulator proteins undergo a dramatic and dynamic spatial reorganization into insulator bodies during osmostress and cell death in a high osmolarity glycerol–p38 mitogen-activated protein kinase–independent manner, leading to a large reduction in DNA-bound insulator proteins that rapidly repopulate chromatin as the bodies disassemble upon return to isotonicity. These bodies occupy distinct nuclear territories and contain a defined structural arrangement of insulator proteins. Our findings suggest insulator bodies are novel nuclear stress foci that can be used as a proxy to monitor the chromatin-bound state of insulator proteins and provide new insights into the effects of osmostress on nuclear and genome organization.

Take a look at a textbook illustration of a cell and you will immediately be able to locate the nucleus, which is often drawn as a spherical or ovoid shaped structure. But not all cells have such nuclei. In fact, some disease states are diagnosed by the presence of nuclei that have an abnormal shape or size. What defines nuclear shape and nuclear size, and how does nuclear geometry affect nuclear function? While the answer to the latter question remains largely unknown, significant progress has been made towards understanding the former. In this review, we provide an overview of the factors and forces that affect nuclear shape and size, discuss the relationship between ER structure and nuclear morphology, and speculate on the possible connection between nuclear size and its shape. We also note the many interesting questions that remain to be explored.

We recently reported on a new wrinkle of complexity in how eukaryotic genes are regulated by providing evidence for a hitherto unknown nuclear function of the signaling kinase, Protein Kinase C-theta (PKC-θ). This chromatin-anchored complex positively regulates inducible immune genes and negatively regulates target miRNA genes. These data challenge the traditional view of mammalian signaling kinases and provides new avenues for therapeutic drug design.

We previously identified a novel non-coding immediate early gene, termed kakusei , from the honeybee (Apis mellifera) and used it as a marker to detect neural activity in the brains of foraging workers (Kiya et al .,2007). Here, we investigated the detailed kakusei gene structure. Expression analysis revealed that, in addition to the neural activity-inducible transcript variant, multiple neural activity-independent transcript variants were constitutively expressed from the same kakusei locus. In situ hybridization revealed that constitutive-type kakusei variants were detected in the whole brain and the RNA was localized predominantly in the neural nuclei, like the inducible-type variant, suggesting the concerted action of inducible- and constitutive-types of kakusei transcript variants on nuclear function.

Recent work has uncovered roles for inositide signalling pathways downstream of phospholipase C activation and inositol 1,4,5-trisphosphate in the regulation of nuclear processes including gene expression, mRNA export and DNA metabolism. The identification of several IPKs (inositol polyphosphate kinases) has renewed interest in the cellular roles of inositol tetra-, penta-, hexa- and pyro-phosphates. Discoveries of inositide receptors and novel mechanisms of inositide action have provided important insights into how such messengers couple to nuclear machinery. In this chapter, we discuss the IPK family members and the nuclear processes that their inositide products regulate.

It is still largely unknown how the various nuclear subcompartments are formed, why they form in particular locations and how they are linked to nuclear function. Nuclear stress bodies provide a new opportunity to address these questions and to test models of self-organization of nuclear structures. The assembly of these bodies requires the synthesis of non-coding RNAs with a probable role in the post-transcriptional regulation of gene expression and in higher-order chromatin organization.

Gender differences in cardiovascular mortality are well documented and oestrogen replacement therapy in post-menopausal women is associated with improved outcomes from cardiovascular events. Indeed, oestrogen therapy has been shown to restore endothelial function in post-menopausal women and reduce the development of atherosclerotic lesions. Despite extensive evidence on the beneficial effect of oestrogen, relatively little is known regarding the molecular signalling mechanism(s) by which oestrogen exerts some of its vascular effects. While the nuclear function of the oestrogen receptor is clearly established, previous studies regarding the membrane and cytoplasmic actions of oestrogen remain inconclusive. Cross-coupling of the oestrogen receptor to phosphoinositide 3-kinase signalling suggests a potentially critical non-nuclear action of the oestrogen receptor and considerably broadens our understanding of the cellular effects of oestrogen.

The meeting ‘The Dynamic Nucleus: Questions and Implications’ took place at Imperial College, London, UK, between June 27 and 29, 2002. It was sponsored by the MRC Clinical Sciences Centre in London and was organized by Niall Dillon and Ana Pombo. ![][1] Over the course of two and a half days, hypotheses and results about the organization and function of the eukaryotic nucleus were discussed intensely in the congenial atmosphere of this meeting. The topics covered ranged from DNA repair to nuclear actin, from nucleolar assembly to the deposition of histone variants, and from technical aspects of fluorescence signal separation to the analysis of chromatin dynamics in living cells. Many nuclear domains have previously been identified (Fig. 1) and recent advances in live‐cell imaging techniques have opened the door for real‐time analyses of the diverse range of nuclear functions associated with these structures. Nearly every major nuclear process was discussed, yet the most novel ideas dealt with the dynamics of nuclear structures and events. New ways to monitor dynamics, paired with the fact that nuclear organization now attracts experts from a wide range of fields, left participants uniformly excited about the potential offered by the marriage of live fluorescence imaging and molecular genetics. A few highlights of the work presented at the meeting follow. Figure 1. Diagram of a mammalian cell nucleus showing many of the nuclear domains that have been identified so far. Although each of these domains can be easily observed by light or electron microscopy approaches, remarkably, a large number of their protein constitutents are highly dynamic. For a detailed overview of these compartments see Spector (2001). ### Rapid diffusion of nuclear factors A large number of studies that monitor fluorescence recovery kinetics of green fluorescent protein (GFP) fusion proteins after photobleaching (FRAP; see Fig. 2) have taught us that nuclear factors are highly dynamic, … [1]: /embed/graphic-1.gif

Posttranscriptional gene regulation relies on hundreds of RNA binding proteins (RBPs) but the function of most RBPs is unknown. The human RBP HuR/ELAVL1 is a conserved mRNA stability regulator. We used PAR-CLIP, a recently developed method based on RNA-protein crosslinking, to identify transcriptome-wide ∼26,000 HuR binding sites. These sites were on average highly conserved, enriched for HuR binding motifs and mainly located in 3' untranslated regions. Surprisingly, many sites were intronic, implicating HuR in mRNA processing. Upon HuR knockdown, mRNA levels and protein synthesis of thousands of target genes were downregulated, validating functionality. HuR and miRNA binding sites tended to reside nearby but generally did not overlap. Additionally, HuR knockdown triggered strong and specific upregulation of miR-7. In summary, we identified thousands of direct and functional HuR targets, found a human miRNA controlled by HuR, and propose a role for HuR in splicing.

Production of estradiol-17β and cAMP was assayed during maturation of the follicle-enclosed oocytes of Xenopus laevis and Rana temporaria stimulated by pituitary suspension or hCG, correspondingly. In some samples, the nuclear function was suppressed by pretreatment with AD. The level of estradiol-17β in the oocytes of the both species was very low and was not affected by hormonal or AD treatment, while the level of cAMP (follicle + medium) increased. When maturation was stimulated by low concentrations of gonadotropic hormones inducing complete or near 100% maturation, the cAMP level increased 1.4- to 3.9-fold. Both higher concentrations of the gonadotropic hormones and pretreatment of the follicles with AD increased the cAMP level still more. Combination of these treatments led to a greater increase of cAMP and to inhibition of oocyte maturation. We conclude that cAMP, rather than estradiol-17β, is involved in the AD-induced inhibition of amphibian oocyte maturation stimulated by gonadotropins. © 1995 Wiley-Liss, Inc.

The microscope has been indispensable to the last century of chromatin structure research. Microscopy techniques have revealed that the three-dimensional location of chromatin is not random but represents a further manifestation of a highly compartmentalized cell nucleus. Moreover, the structure and location of genetic loci display cell type-specific differences and relate directly to the state of differentiation. Advances to bridge imaging with genetic, molecular and biochemical approaches have greatly enhanced our understanding of the interdependence of chromatin structure and nuclear function in mammalian cells. In this review we discuss the current state of chromatin structure research in relationship to the variety of microscopy techniques that have contributed to this field.

In this paper, we used gait silhouettes that provided by CASIA, and all we study are based on this database. Firstly, we normalized and centralized gait silhouettes and get the gait sequence, secondly, we extract the active regions by calculating the difference of two adjacent silhouettes images, and construct an AEI by accumulating these active regions, finally, using Kernel Discriminant Analysis (KDA) method to analysis the AEI, and parameter optimization method used to determine the nuclear function of KDA, and using SVM to classified and recognized gait. Experimental results show that such methods to be identified effective.

Like many other cells, mammalian cardiac cells are able to divide and proliferate during development and during a short time after birth. However, the ability to divide decreases dramatically in the neonatal period, and adult cardiomyocytes are unable to proliferate. In contrast, postnatal cardiomyocytes from some lower vertebrates (e.g., zebrafish, newt) maintain the capability to divide, although the mechanisms underlying these species differences are unknown.

When theoretical physicists predicted a real possibility of nuclear explosives in the 1940s, it set a precedent for the level of government commitment to ideas from the scientific community. The UK and the US proceeded to launch huge "all-or-nothing" ventures based purely on theory. A whole industry had to be created before one demonstration could be attempted; the inherent critical mass for fission allowed nothing less. Where-as government decision was driven by fear of overwhelming disadvantage, responsibility for its technical justification lay with theoretical physicists whose initial predictive theory of nuclear function had to be sound enough to support that decision.

High-throughput DNA sequencing approaches have enabled direct interrogation of chromatin samples from mammalian cells. We are beginning to develop a genome-wide description of nuclear function during development, but further data collection, refinement, and integration are needed.

In the past 20 years cell biologists have studied the cell nucleus extensively, aided by advances in cell imaging technology and microscopy. Consequently, the volume of image data of the cell nucleus – and the compartments it contains – is growing rapidly. The spatial organisation of these nuclear compartments is thought to be fundamentally associated with nuclear function. However, the rules that oversee nuclear architecture remain unclear and controversial. As a result, there is an increasing need to replace qualitative visual assessment of microscope images with quantitative and automated methods. Such tools can substantially reduce manual labour and more importantly remove subjective bias. Quantitative methods can also increase the accuracy, sensitivity and reproducibility of data analysis. In this paper, we describe image processing and analysis methodology for the investigation of nuclear architecture, and the application of these methods to quantitatively explore the promyelocytic leukaemia (PML) nuclear bodies (NBs). PML NBs are linked with numerous nuclear functions including transcription and protein degradation. However, we know very little about the three-dimensional (3-D) architecture of PML NBs in relation to each other or within the general volume of the nucleus. Finally, we emphasise methods for the analysis of replicate images (of a given nuclear compartment across different cell nuclei) in order to aggregate information about nuclear architecture.