Three-dimensional chromatin organization in brain function and dysfunction

The three-dimensional (3D) organization of chromatin within the nucleus is now recognized as a bona fide epigenetic property influencing genome function, replication, and maintenance. In the recent years, several studies have revealed how 3D chromatin organization is associated with brain function and its emerging role in disorders of the brain. 3D chromatin organization plays a crucial role in the development of different cell types of the nervous system and some neuronal cell types have adapted unique modifications to this organization that deviates from all other cell types. In post-mitotic neurons, dynamic changes in chromatin interactions in response to neuronal activity underlie learning and memory formation. Finally, new evidence directly links 3D chromatin organization to several disorders of the brain. These recent findings position 3D chromatin organization as a fundamental regulatory mechanism poised to reveal the etiology of brain function and dysfunctions.     

Large-scale chromatin fibers of living cells display a discontinuous functional organization

We investigated the chromatin organization of living cells with a combination of recently developed approaches for histone and DNA labeling. Nucleosomal DNA was labeled with a histone H2B-GFP (green fluorescent protein) fusion protein and the chromatin organization of living HeLa cells was analyzed by high resolution confocal microscopy. Within the perinuclear and perinucleolar regions chromatin was organized into large-scale fibers of 2 to 8 microm in length and 300 to 500 nm in diameter. Within the nuclear interior we observed similar large-scale fibers, but in addition focal as well as diffuse forms of organization. Comparison with standard labeling and detection procedures revealed major differences in the chromatin organization observed. Chromatin organization revealed by the distribution of histone H2B-GFP was directly compared with the functional organization of chromatin by Cy3-dUTP labeling of DNA replicating at a specific time. DNA regions replicating at a specific time display characteristic physical and functional properties. Analysis of Cy3-labeled foci revealed that they are associated with all three forms of chromatin organization (fibrillar, focal and diffuse). In particular, Cy3-labeled foci appeared as discontinuous regions of large-scale fibers. These results demonstrate that large-scale chromatin fibers have discontinuous functional characteristics.     

TPA induces simultaneous alterations in the synthesis and organization of vimentin

We have found an increased rate of vimentin synthesis in TPA-treated chicken embryonic fibroblasts, as shown by two-dimensional electrophoretic separation of newly synthesized polypeptides. The capacity of TPA to elicit this effect correlated with its activity as a tumor promoter. Treatment with TPA also altered the organization of the vimentincontaining intermediate filaments, as revealed by immunofluorescence. Treatments which inhibited the TPA-induced rearrangements of vimentin filaments did not prevent the increase in the rate of vimentin synthesis, indicating that gross alterations in cytoskeletal organization were not the immediate cause of the altered vimentin synthesis. On the other hand, alterations in the rate of vimentin synthesis may be a necessary, but not sufficient condition for alterations in vimentin filament organization. TPA as a positive modulator of vimentin synthesis may serve as a useful probe for an eventual understanding of the dynamics of the mechanisms that control the assembly and organization of vimentin filaments.     

Is an orthorhombic lateral packing and a proper lamellar organization important for the skin barrier function?

The lipid organization in the stratum corneum (SC), plays an important role in the barrier function of the skin. SC lipids form two lamellar phases with a predominantly orthorhombic packing. In previous publications a lipid model was presented, referred to as the stratum corneum substitute (SCS), that closely mimics the SC lipid organization and barrier function. Therefore, the SCS serves as a unique tool to relate lipid organization with barrier function. In the present study we examined the effect of the orthorhombic to hexagonal phase transition on the barrier function of human SC and SCS. In addition, the SCS was modified by changing the free fatty acid composition, resulting in a hexagonal packing and perturbed lamellar organization. By measuring the permeability to benzoic acid as function of temperature, Arrhenius plots were constructed from which activation energies were calculated. The results suggest that the change from orthorhombic to hexagonal packing in human SC and SCS, does not have an effect on the permeability. However, the modified SCS revealed an increased permeability to benzoic acid, which we related to its perturbed lamellar organization. Thus, a proper lamellar organization is more crucial for a competent barrier function than the presence of an orthorhombic lateral packing.     

Calcium transients regulate titin organization during myofibrillogenesis

Titin has a Ca2+-dependent kinase domain and may act as a molecular template for myofibrillogenesis. Therefore, we examined the relationship between endogenous Ca2+ transients and titin organization in embryonic myocytes. When transients were blocked during sarcomere assembly, titin organization was disrupted. Titin was distributed in punctate aggregates on an otherwise diffuse background, resulting in a 66% decrease in organization. Myosin, as reported previously, was also disrupted in a similar manner (75% decrease). In titin-actin-myosin triple-labeling experiments, myosin and titin were highly colocalized, although titin aggregates without significant myosin accumulation were also observed. This suggests that myosin-titin association is not dependent on Ca2+ transients, although terminal aspects of titin-myosin organization require transients. We also examined whether titin organization is dependent on actin filament dynamics. The data indicate that (1) the normal sarcomeric arrangement of titin depends on Ca2+ transients, (2) titin-myosin association does not require Ca2+ transients, and (3) titin filament organization does not depend on barbed-end actin dynamics.     

Beyond the sequence: cellular organization of genome function

Genomes are more than linear sequences. In vivo they exist as elaborate physical structures, and their functional properties are strongly determined by their cellular organization. I discuss here the functional relevance of spatial and temporal genome organization at three hierarchical levels: the organization of nuclear processes, the higher-order organization of the chromatin fiber, and the spatial arrangement of genomes within the cell nucleus. Recent insights into the cell biology of genomes have overturned long-held dogmas and have led to new models for many essential cellular processes, including gene expression and genome stability.     

Use of biomolecular templates for the fabrication of metal nanowires

The nano-scale spatial organization of metallic and other inorganic materials into 1D objects is a key task in nanotechnology. Nano-scale fibers and tubes are very useful templates for such organization because of their inherent 1D organization. Fibrillar biological molecules and biomolecular assemblies are excellent physical supports on which to organize the inorganic material. Furthermore, these biological assemblies can facilitate high-order organization and specific orientation of inorganic structures by their utilization of highly specific biological recognition properties. In this minireview, I will describe the use of biomolecules and biomolecular assemblies, including DNA, proteins, peptides, and even viral particles, which are excellent templates for 1D organization of inorganic materials into wires. This ranges from simple attempts at electroless deposition on inert biological templates to the advanced use of structural motifs and specific protein-DNA interactions for nano-bio-lithography as well as the fabrication of multilayer organic and inorganic composites. The potential technological applications of these hybrid biological-inorganic assemblies will be discussed.     

钙信号基本单位和特征的研究进展

细胞内存在多种不同的Ｃａ＾２＋信号基本单位,这些Ｃａ＾２＋信号基本单位依赖于刺激浓度的等级体系组织。低水平的刺激激活单通道开放,产生Ｃａ＾２＋脉冲或Ｃａ＾２＋夸克;在等组织水平刺激则产生喷烟和火花,似乎与一小簇通道的激活有关;高浓度刺激时,Ｃａ＾２＋信号基本单位协同产生球形Ｃａ＾２＋波。这些Ｃａ＾２＋基本单位既本现了钙释放单位（Ｃａ＾２＋ｒｅｌｅａｓｅ ｕｎｉｔ）的特征,又导致Ｃａ＾２＋信号传播在     

The causes and scope of political egalitarianism during the Last Glacial: a multi-disciplinary perspective

This paper reviews and synthesizes emerging multi-disciplinary evidence toward understanding the development of social and political organization in the Last Glacial. Evidence for the prevalence and scope of political egalitarianism is reviewed and the biological, social, and environmental influences on this mode of human organization are further explored. Viewing social and political organization in the Last Glacial in a much wider, multi-disciplinary context provides the footing for coherent theory building and hypothesis testing by which to further explore human political systems. We aim to overcome the claim that our ancestors’ form of social organization is untestable, as well as counter a degree of exaggeration regarding possibilities for sedentism, population densities, and hierarchical structures prior to the Holocene with crucial advances from disparate disciplines.     

Chromatin Architecture in the Fly: Living without CTCF/Cohesin Loop Extrusion?

The organization of the genome into topologically associated domains (TADs) appears to be a fundamental process occurring across a wide range of eukaryote organisms, and it likely plays an important role in providing an architectural foundation for gene regulation. Initial studies emphasized the remarkable parallels between TAD organization in organisms as diverse as Drosophila and mammals. However, whereas CCCTC‐binding factor (CTCF)/cohesin loop extrusion is emerging as a key mechanism for the formation of mammalian topological domains, the genome organization in Drosophila appears to depend primarily on the partitioning of chromatin state domains. Recent work suggesting a fundamental conserved role of chromatin state in building domain architecture is discussed and insights into genome organization from recent studies in Drosophila are considered.     

The systems organization of human functions: the theoretical aspects

On the basis of the theory of functional systems, suggested by P. K. Anokhin, leading principals of system organization of human functions are regarded. General characteristics of functional systems are stated. Some peculiarities of intrasystem and intersystem organization of functional systems of human organism are discovered. The role of functional systems in organization of normal human live activity as well as under psychoemotional stress and pathology is shown. System principals of compensation of disordered functions during rehabilitation of persons undergone stresses and ecologically unfavorable loads are considered.     

Spatial order as a source of kinetic cooperativity in organized bound enzyme systems.

When enzyme molecules are distributed within a negatively charged matrix, the kinetics of the conversion of a negatively charged substrate into a product depends on the organization of fixed charges and bound enzyme molecules. Organization is taken to mean the existence of macroscopic heterogeneity in the distribution of fixed charge density, or of bound enzyme density, or of both. The degree of organization is quantitatively expressed by the monovariate moments of charge and enzyme distributions as well as by the bivariate moments of these two distributions. The overall reaction rate of the bound enzyme system may be expressed in terms of the monovariate moments of the charge density and of the bivariate moments of charge and enzyme densities. The monovariate moments of enzyme density do not affect the reaction rate. With respect to the situation where the fixed charges and enzyme molecules are randomly distributed in the matrix, the molecular organization, as expressed by these two types of moments, generates an increase or decrease of the overall reaction rate as well as a cooperativity of the kinetic response of the system. Thus both the alteration of the rate and the modulation of cooperativity are the consequence of a spatial organization of charges with respect to the enzyme molecules. The rate equations have been derived for different types of organization of fixed charges and enzyme molecules, namely, clustered charges and homogeneously distributed enzyme molecules, clustered enzyme molecules and homogeneously distributed charges, clusters of charges and clusters of enzymes that partly overlap, and clusters of enzymes and clusters of charges that are exactly superimposed. Computer simulations of these equations show how spatial molecular organization may modulate the overall reaction rate.     

African Political Models in the American Southwest: Hopi as an Internal Frontier Society

Most ethnological and archeological analyses of Pueblo social organization derive its particular character from the need to adapt to an arid environment. This article challenges an ecological interpretation (without dismissing ecological constraints), finding similarities between the organization of one Pueblo society, the Hopi, and features of what Kopytoff calls "internal frontier societies" in Africa. Hopi political and ceremonial organization is viewed as responding to "internal frontier" migrations.     

A Crowdsourced nucleus: Understanding nuclear organization in terms of dynamically networked protein function

The spatial organization of the nucleus results in a compartmentalized structure that affects all aspects of nuclear function. This compartmentalization involves genome organization as well as the formation of nuclear bodies and plays a role in many functions, including gene regulation, genome stability, replication, and RNA processing. Here we review the recent findings associated with the spatial organization of the nucleus and reveal that a common theme for nuclear proteins is their ability to participate in a variety of functions and pathways. We consider this multiplicity of function in terms of Crowdsourcing, a recent phenomenon in the world of information technology, and suggest that this model provides a novel way to synthesize the many intersections between nuclear organization and function. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.     

An inventory of the bacterial macromolecular components and their spatial organization

Formerly regarded as small 'bags' of nucleic acids with randomly diffusing enzymes, bacteria are organized by a sophisticated and tightly regulated molecular machinery. Here, we review qualitative and quantitative data on the intracellular organization of bacteria and provide a detailed inventory of macromolecular structures such as the divisome, the degradosome and the bacterial 'nucleolus'. We discuss how these metabolically active structures manage the spatial organization of the cell and how macromolecular crowding influences them. We present for the first time a visualization program, lifeexplorer, that can be used to study the interplay between metabolism and spatial organization of a prokaryotic cell.     

Convergent evolution of clustering of Iroquois homeobox genes across metazoans

Vertebrate and Drosophila Iroquois genes are organized in clusters of 3 genes sharing blocks of conserved regulatory sequences. Here, we report a 3-gene cluster in the basal, preduplicative chordate amphioxus. Surprisingly, however, the origin of the amphioxus cluster is independent of those in vertebrates and drosophilids. Investigation of genomic organization of Iroquois genes in other 17 metazoan genomes revealed a fourth independent 3-gene cluster organization in polychaetes, as well as additional 2- and 4-gene clusters in other clades, in one of the most striking examples of convergence in genomic organization described so far. The recurrent independent evolution of Iroquois clusters suggests a functional importance of this organization for these genes, perhaps related to the sharing of regulatory elements. Consistent with this, comparative analysis of genomic regions flanking the 3 amphioxus Irx genes revealed several blocks of sequences, conserved for at least 100 Myr. Finally, we discuss the possible causes and implications of the convergent evolution of this genomic and regulatory organization throughout metazoans.