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Nuclear Architecture And Dynamics

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Nuclear Architecture and Dynamics

Nuclear Architecture and Dynamics Book
Author : Christophe Lavelle,Jean-Marc Victor
Publisher : Academic Press
Release : 2017-10-27
ISBN : 012803503X
Language : En, Es, Fr & De

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Book Description :

Nuclear Architecture and Dynamics provides a definitive resource for (bio)physicists and molecular and cellular biologists whose research involves an understanding of the organization of the genome and the mechanisms of its proper reading, maintenance, and replication by the cell. This book brings together the biochemical and physical characteristics of genome organization, providing a relevant framework in which to interpret the control of gene expression and cell differentiation. It includes work from a group of international experts, including biologists, physicists, mathematicians, and bioinformaticians who have come together for a comprehensive presentation of the current developments in the nuclear dynamics and architecture field. The book provides the uninitiated with an entry point to a highly dynamic, but complex issue, and the expert with an opportunity to have a fresh look at the viewpoints advocated by researchers from different disciplines. Highlights the link between the (bio)chemistry and the (bio)physics of chromatin Deciphers the complex interplay between numerous biochemical factors at task in the nucleus and the physical state of chromatin Provides a collective view of the field by a large, diverse group of authors with both physics and biology backgrounds

Nuclear Architecture and Dynamics of Stably Integrated Retroviral Sequences

Nuclear Architecture and Dynamics of Stably Integrated Retroviral Sequences Book
Author : Jens Nagel
Publisher : Unknown
Release : 2011
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Nuclear Architecture and Dynamics of Stably Integrated Retroviral Sequences book written by Jens Nagel, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Dynamics and Manipulation of Nuclear Architecture and Gene Expression

Dynamics and Manipulation of Nuclear Architecture and Gene Expression Book
Author : Katharina Thanisch
Publisher : Unknown
Release : 2015
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Dynamics and Manipulation of Nuclear Architecture and Gene Expression book written by Katharina Thanisch, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Nuclear Architecture and Structural Dynamics

Nuclear Architecture and Structural Dynamics Book
Author : Josef H. Exler
Publisher : Unknown
Release : 2010
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Nuclear Architecture and Structural Dynamics book written by Josef H. Exler, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Nuclear Architecture Dynamics in Tadpole Tail Regeneration

Nuclear Architecture Dynamics in Tadpole Tail Regeneration Book
Author : Jessica Kay Chang
Publisher : Unknown
Release : 2019
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Mammals possess very limited regeneration capabilities, where the few examples of scarless healing tend to be restricted to early development. In light of this, it is of great interest to study animals that can faithfully regrow complete appendages, and uncover the biological properties that facilitate regeneration. Xenopus tropicalis is an excellent vertebrate model of regeneration, as tadpoles rapidly regenerate amputated tails, a process that has an interesting developmental history that may be widely informative as to why mammals selectively heal through scarring as they age. Though we have some understanding of what processes are required for tail regeneration, we have yet to systematically chronicle the molecular and regulatory events that must set up an apparently coordinated response. In this dissertation, I address two primary questions in the field of regeneration—what molecular events occur in the first 24 hours to set up a potent regenerative bud, and how is this process regulated? In Chapter 2, I chronicle the transcriptional history of tadpole tail regeneration, focusing primarily within the first 24 hours post amputation. In Chapter 3, I describe a novel nuclear morphology I identified in the tadpole tail, detail how nuclei change shape as an early regeneration response, and investigate the relationship between nuclear shape and chromatin state. Finally, in Chapter 4, I address several future directions with respect to this thesis.

Chromatin Regulation and Dynamics

Chromatin Regulation and Dynamics Book
Author : Anita Göndör
Publisher : Academic Press
Release : 2016-10-25
ISBN : 0128034025
Language : En, Es, Fr & De

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Book Description :

Chromatin Regulation and Dynamics integrates knowledge on the dynamic regulation of primary chromatin fiber with the 3D nuclear architecture, then connects related processes to circadian regulation of cellular metabolic states, representing a paradigm of adaptation to environmental changes. The final chapters discuss the many ways chromatin dynamics can synergize to fundamentally contribute to the development of complex diseases. Chromatin dynamics, which is strategically positioned at the gene-environment interface, is at the core of disease development. As such, Chromatin Regulation and Dynamics, part of the Translational Epigenetics series, facilitates the flow of information between research areas such as chromatin regulation, developmental biology, and epidemiology by focusing on recent findings of the fast-moving field of chromatin regulation. Presents and discusses novel principles of chromatin regulation and dynamics with a cross-disciplinary perspective Promotes crosstalk between basic sciences and their applications in medicine Provides a framework for future studies on complex diseases by integrating various aspects of chromatin biology with cellular metabolic states, with an emphasis on the dynamic nature of chromatin and stochastic principles Integrates knowledge on the dynamic regulation of primary chromatin fiber with 3D nuclear architecture, then connects related processes to circadian regulation of cellular metabolic states, representing a paradigm of adaptation to environmental changes

Nuclear Dynamics

Nuclear Dynamics Book
Author : K. Nagata,K. Takeyasu
Publisher : Springer Science & Business Media
Release : 2007-12-03
ISBN : 9784431301301
Language : En, Es, Fr & De

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Book Description :

The dynamics of nuclear structures described in this book furnish the basis for a comprehensive understanding of how the higher-order organization and function of the nucleus is established and how it correlates with the expression of a variety of vital activities such as cell proliferation and differentiation. The resulting volume creates an invaluable source of reference for researchers in the field.

Dynamics of Nuclear Architecture of Oocytes Throughout Folliculogenesis and Embryos During Preimplantation Development in the Mouse

Dynamics of Nuclear Architecture of Oocytes Throughout Folliculogenesis and Embryos During Preimplantation Development in the Mouse Book
Author : Valeria Merico
Publisher : Unknown
Release : 2004
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Dynamics of Nuclear Architecture of Oocytes Throughout Folliculogenesis and Embryos During Preimplantation Development in the Mouse book written by Valeria Merico, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Visualizing the Dynamics of 4D Nuclear Architecture During Enhancer Promoter Transcription Activation Using Live Imaging Techniques

Visualizing the Dynamics of 4D Nuclear Architecture During Enhancer Promoter Transcription Activation Using Live Imaging Techniques Book
Author : Leah Kim
Publisher : Unknown
Release : 2020
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

The transcription machinery requires spatiotemporal coordination of its regulatory elements for precise gene expression. It is believed that the dynamics in the nuclear architecture like enhancer:promoter looping interaction is essential for the regulation of the transcription machinery. However, the detail of the change in 4D nuclear architecture during transcription is poorly understood. Here we seek to visualize a pair of enhancer and its associated target gene based on a real time, live cell imaging that uses optimized CRISPR-Cas9 and MS2/PP7 system. Our prior work on measuring TFF1 transcription bursting in MCF7 cells confirmed the efficiency and sensitivity of our imaging techniques. In this study, we aim to visualize c-MYC enhancer(c-MYCe) and c-MYC gene in live HeLa cells based on our preliminary data proving that c-MYC enhancer is a functional enhancer. We plan to measure the relative timing of signal, the duration of activity, and the distribution of intensity over the course of activity. The spatial kinetics between c-MYCe and c-MYC over time will be measured, and their motion relative to transcriptional activity (on/off signal) will be examined. Collectively, we hope to advance the understanding of the precise 4D dynamics of the events underlying enhancer-mediated transcription regulation.

Nuclear Dynamics of Radiation induced Foci in Euchromatin and Heterochromatin

Nuclear Dynamics of Radiation induced Foci in Euchromatin and Heterochromatin Book
Author : Anonim
Publisher : Unknown
Release : 2013
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Repair of double strand breaks (DSBs) is essential for cell survival and genome integrity. While much is known about the molecular mechanisms involved in DSB repair and checkpoint activation, the roles of nuclear dynamics of radiation-induced foci (RIF) in DNA repair are just beginning to emerge. Here, we summarize results from recent studies that point to distinct features of these dynamics in two different chromatin environments: heterochromatin and euchromatin. We also discuss how nuclear architecture and chromatin components might control these dynamics, and the need of novel quantification methods for a better description and interpretation of these phenomena. These studies are expected to provide new biomarkers for radiation risk and new strategies for cancer detection and treatment.

Nuclear Envelope Dynamics in Embryos and Somatic Cells

Nuclear Envelope Dynamics in Embryos and Somatic Cells Book
Author : Philippe Collas
Publisher : Springer
Release : 2012-11-01
ISBN : 9781461349372
Language : En, Es, Fr & De

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Book Description :

This volume provides an exhaustive review of the most current knowledge of the composition, architecture and dynamics of the nuclear envelope. In contrast to other comprehensive works on cellular membranes in general, this book is the first to specifically address the nuclear envelope. Experts in the field relate the different domains of the nuclear envelope, their biogenesis, their composition, their mode of targeting to chromosomes and how they dissociate from chromosomes upon cell division. A wealth of information from several experimental systems is provided, such as dividing somatic cells, embryos and nuclear assembly assays in cell-free extracts, in a wide range of vertebrate and invertebrate organisms ranging from humans to yeast. The book also contains up-to-date reviews on the relationship between mutations in proteins of the nuclear envelope and Emery-Dreifuss muscular dystrophy. The breadth of topics covered in what may seem to be a field as narrow as the nuclear envelope makes this volume a valuable reference.

Organization Dynamics and Modification of Chromatin in Plants

Organization  Dynamics and Modification of Chromatin in Plants Book
Author : A. Houben,T. Naranjo,M. J. Puertas
Publisher : Unknown
Release : 2014-08-19
ISBN : 9783318027259
Language : En, Es, Fr & De

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Book Description :

This special topic issue is divided into two sections, and each of them presents its own set of reviews and research articles. 'Organization and dynamics of plant chromatin' is the title of the first section which explores an ample variety of subjects. The topics covered include the structure and function of meiotic chromosomes, open chromatin, nuclear architecture and chromatin dynamics and proteomic analysis of plant cell nuclei. 'Epigenetic modification of plant chromatin' is the title of the second section. This provides a broad array of studies on various plant species and epigenetic modification of plant chromatin. This novel approach represents one of the most interesting developments in research in the field of modern cytogenetics.'Organization, Dynamics and Modification of Chromatin in Plants' is of particular interest to researchers and teachers in genetics and cytology.

Advances in Nuclear Architecture

Advances in Nuclear Architecture Book
Author : Niall M. Adams,Paul S. Freemont
Publisher : Springer Science & Business Media
Release : 2010-10-17
ISBN : 9789048198993
Language : En, Es, Fr & De

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Book Description :

This book provides a snapshot of the state-of-the art in the study of mammalian cell nuclear architecture, and features a diverse range of chapters written by top researchers. A key aspect is an emphasis on precise and repeatable quantitative analysis and simulation in addition to the more familiar biological perspective. The fusion of such material frames the future of the discipline. Quantitative contributions stress reproducible and robust 3D analysis, using a variety of tools ranging from point pattern analysis to shape registration methods. Biological insights include the role of nuclear subdomains in cancer, nuclear molecular motors, and a holistic view of gene transcription.

Nuclear Architecture in Normal and Cloned Bovine Early Embryos

Nuclear Architecture in Normal and Cloned Bovine Early Embryos Book
Author : Andrey Pichugin
Publisher : Unknown
Release : 2008
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Developmental reprogramming during mammalian fertilization and pre-implantation development in in vitro fertilized (IVF) embryos is a complex process that allows the highly differentiated gametes to revert to undifferentiated cell types following syngamy and then gradually differentiate into individual cell lineages. These processes involve changes in chromatin structure, in global epigenetic modifications and in nuclear architecture of embryonic nuclei. The objective of the present study was to develop approaches for understanding these series of phenomena in early embryos. We used the possibility to compare normal (IVF) and nuclear tranfer (NT) embryos in bovine species where the pre-implantation development is long enough to assess the nuclear dynamics of reprogramming events before major embryonic genome activation. In a first approach, we studied the establishment of heterochromatin pattern specific for embryo during the reprogramming period in IVF and NT bovine embryos. We applied two markers of pericentric heterochromatin: heterochromatin protein 1 (HP1beta) and tri methylated histone H3 (H3K9me3); and a marker of centromeres (CENPA/B), in order to characterize structural parameters of constitutive heterochromatin in early stages of development. Using immunofluorescence technique, we were able to observe dynamic changes in heterochromatin organization in connection with embryos origin. In IVF and some NT embryos, heterochromatin was observed in dispersed state up to the 8-cell stage, and then in a condensed pattern corresponding to the well characterized chromocenters constituted by blocks of HP1beta and H3K9me3 associated with centromeres. However, a significant part of NT embryos underwent an altered dynamics of heterochromatinization characterized by a precocious heterochromatin condensation as soon as the 2-cell stage. In a second approach, we used senescent somatic cells as donors for nuclear transfer experiments in order to assess the influence of structural organization of donor cell nucleus on structural organization of nuclei in cloned embryos. Surprisingly, the large-scale three-dimensional arrangement of heterochromatin within the senescent-NT nucleus recapitulated the dynamics observed in IVF or somatic non-senescent NT embryos, with comparable percentages of embryos with dispersed and precociously condensed heterochromatin similar to those observed in the previous investigation. These results suggest that a robust process of epigenetic reprogramming is piloted by bovine oocyte in early embryos. The altered kinetics in genome restructuring in some NT embryos might be linked to the precocious transcriptional activation and precocious increase of DNA methylation level reported in other studies. The present work allowed us to point out the distinction between NT embryos with correct developmental reprogramming and abnormal, at least temporally, epigenetic reprogramming, as well as to demonstrate that the impact of nuclear organization of heterochromatin in the donor cell on structural organization of nucleus in NT embryos is relatively low. This may account for the relatively high development efficiency in bovine cloning as compared to other species.

High content and Super resolution Microscopy Reveals the Dynamic Nuclear Architecture Aand Mobile Epigenetic Marks in Plasmodiumfalciparum

High content and Super resolution Microscopy Reveals the Dynamic Nuclear Architecture Aand Mobile Epigenetic Marks in Plasmodiumfalciparum Book
Author : Caron Griffiths (A.)
Publisher : Unknown
Release : 2013
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

The malaria-causing parasite Plasmodium falciparum 1s dependent on tightly regulated gene expression for its progression through the intra-erythrocytic life cycle, pathogenesis and establishment of persistent infection by evasion of the human host's immune system. Evidence points towards P. falciparum being unusually dependent on nuclear architecture and genomic organisation for the control of gene expression. Spatially defined nuclear regions of transcriptional activity have been detected and the spatial positioning of loci may determine their transcriptional potential. Additionally, a number of epigenetic markers have been shown to occupy spatially distinct subcompartments of the nuclear volume. Limitations of microscopic assays used until now have left us with a stereotyped and incomplete image of the organisation of the parasite nucleus and the transcriptional and epigenetic factors involved in the regulation of parasite gene expression, and the possible dynamics thereof. This work focused on the use of high-content and super-resolution fluorescent microscopy for the study and graphical representation of the spatial organisation of various nuclear factors involved in transcriptional regulation in P. falciparum parasites. The first objective (chapter 2) establishes P. falciparum parasite sample preparation and fluorescent labeling techniques for microscopy. Immunofluorescent labeling of var gene associated transcription repressive and permissive histone modifications, H3K9me3 and H3K9ac, respectively, as well as serine 2- phosphorylated RNA polymerase II and the putative transcription and splicing factor PfMyb2, was optimised. DNA fluorescent in situ hybridisation was also optimised for labeling of var gene exons. In the second objective (chapter 3), the assays established in the previous chapter are used for high-content combinatorial labeling in thousands of nuclei, followed by analysis using a bespoke computational algorithm for the detection and classification of different labeling patterns. This approach revealed a high level of diversity in the nuclear distributions of each assayed target. Superresolution stochastic optical reconstruction microscopy was used to further study the sub-diffraction organisation of selected labeling patterns. The data presented in this dissertation reveal that the complex spatial organisation of certain nuclear factors is subject to greater diversity within the nucleus of P. falciparum parasites than previously thought.

Modelling Nuclear Body Dynamics in Living Cells by 4 D Microscopy Image Analysis and Simulation

Modelling Nuclear Body Dynamics in Living Cells by 4 D Microscopy  Image Analysis and Simulation Book
Author : Anonim
Publisher : Unknown
Release : 2003
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

The work presented here demonstrates rules of and validates models for nuclear body (NB) dynamics. Simulation tools developed in the course of this work can be used in future work to generate hypotheses about related aspects of nuclear architecture. Initially I examined the mobility of vimentin nuclear bodies bodies (VNB) in interphase by single particle tracking and analysis of fluorescence images from 4-D confocal laser scanning microscopy (CLSM). These synthetic nuclear bodies are observed in cells transfected with labelled nuclear-targeted Xenopus laevis vimentin. Analysis shows that VNBs undergo anomalous diffusion in the nuclei, independent of metabolic energy. Individual bodies display either one of the three modes of diffusion -- directed, restricted or simple. The consistency of modes and magnitudes of diffusion constants between VNBs and bona fide nuclear bodies points to a generic mechanism that mediates and regulates the mobility of nuclear bodies. Since the results of diffusion analysis of VNBs did not agree with a simple diffusion model, I tested the alternative interchromosomal domain (ICD) compartment model. The ICD model predicts that in interphase cell nuclei, individual decompacted chromosomes do not intermingle, but are separated by a significant interchromatin space forming a network of channels. These networks could affect the mobility of nuclear bodies. Monte Carlo simulations that predict the effects of channels and other obstructions on NB diffusion were tested, but they could not explain deviation from ideal behaviour. Fitting an empirical model of `critical diffusion' produced similar results. Therefore the ICD model as a purely obstructing network of channels needs modification, to possibly include binding. To examine the role of chromatin density in intra-nuclear diffusion, I employed multidimensional fluorescence recovery after photobleaching (FRAP) in living cells. The influence of chromatin density on diffusive mobility of the nuclear.

Quantitative Analysis of Chromatin Dynamics and Nuclear Geometry in Living Yeast Cells

Quantitative Analysis of Chromatin Dynamics and Nuclear Geometry in Living Yeast Cells Book
Author : Renjie Wang
Publisher : Unknown
Release : 2016
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Chromosome high-order architecture has been increasingly studied over the last decade thanks to technological breakthroughs in imaging and in molecular biology. It is now established that structural organization of the genome is a key determinant in all aspects of genomic transactions. Although several models have been proposed to describe the folding of chromosomes, the physical principles governing their organization are still largely debated. Nucleus is the cell's compartment in which chromosomal DNA is confined. Geometrical constrains imposed by nuclear confinement are expected to affect high-order chromatin structure. However, the quantitative measurement of the influence of the nuclear structure on the genome organization is unknown, mostly because accurate nuclear shape and size determination is technically challenging. This thesis was organized along two axes: the first aim of my project was to study the dynamics and physical properties of chromatin in the S. cerevisiae yeast nucleus. The second objective I had was to develop techniques to detect and analyze the nuclear 3D geomtry with high accuracy. Ribosomal DNA (rDNA) is the repetitive sequences which clustered in the nucleolus in budding yeast cells. First, I studied the dynamics of non-rDNA and rDNA in exponentially growing yeast cells. The motion of the non-rDNA could be modeled as a two-regime Rouse model. The dynamics of rDNA was very different and could be fitted well with a power law of scaling exponent ~0.7. Furthermore, we compared the dynamics change of non-rDNA in WT strains and temperature sensitive (TS) strains before and after global transcription was actived. The fluctuations of non-rDNA genes after transcriptional inactivation were much higher than in the control strain. The motion of the chromatin was still consistent with the Rouse model. We propose that the chromatin in living cells is best modeled using an alternative Rouse model: the "branched Rouse polymer". Second, we developed "NucQuant", an automated fluorescent localization method which accurately interpolates the nuclear envelope (NE) position in a large cell population. This algorithm includes a post-acquisition correction of the measurement bias due to spherical aberration along Z-axis. "NucQuant" can be used to determine the nuclear geometry under different conditions. Combined with microfluidic technology, I could accurately estimate the shape and size of the nuclei in 3D along entire cell cycle. "NucQuant" was also utilized to detect the distribution of nuclear pore complexes (NPCs) clusters under different conditions, and revealed their non-homogeneous distribution. Upon reduction of the nucleolar volume, NPCs are concentrated in the NE flanking the nucleolus, suggesting a physical link between NPCs and the nucleolar content. In conclusion, we have further explored the biophysical properties of the chromatin, and proposed that chromatin in the nucleoplasm can be modeled as "branched Rouse polymers". Moreover, we have developed "NucQuant", a set of computational tools to facilitate the study of the nuclear shape and size. Further analysis will be required to reveal the links between the nucleus geometry and the chromatin dynamics.

Chemical Abstracts

Chemical Abstracts Book
Author : Anonim
Publisher : Unknown
Release : 2002
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Chemical Abstracts book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.