The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context.

4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.

[Stress echocardiography and its central role in cardiac diagnostics]. / Stressechokardiographie und ihre zentrale Rolle in der kardiologischen Diagnostik.

Stress echocardiography (SE) has an established central role as a diagnostic tool in cardiology. It is not only an established method for the diagnostic and prognostic stratification of patients with coronary artery disease but also shows an emerging value for assessment of cardiac function beyond coronary artery disease. The enormous conceptual technological development of ultrasound technology (Doppler, digitizing, tissue Doppler imaging, strain technology, 3­D-echo and new ultrasound contrast agents) has led to applications of SE in almost all diagnostic fields of cardiology. The use of SE provides not only the possibility to identify coronary stenosis but also to evaluate the function of the microvasculature and heart valves, to detect possible pulmonary hypertension and also to test the systolic/diastolic reaction/mechanics of the right/left ventricle (LV/RV) and left atrium (LA) in response to load. Further developments of ultrasound technology enable better temporal resolution and contemporary analyses of cardiac mechanics of the LV/RV and LA. Pharmacological stress echocardiography extends the diagnostic field to patients who are not able to endure physical stress. SE represents an environmentally friendly, patient-friendly, cost-efficient and radiation-free examination method; however, SE requires extensive basic training as well as continuous training of the examiner to ensure that all possible advantages of the method can be utilized to the benefit of patients.

Interfaces of ionic liquids and transition metal surfaces-adsorption, growth, and thermal reactions of ultrathin [C1C1Im][Tf2N] films on metallic and oxidised Ni(111) surfaces.

Ultrathin films of the ionic liquid 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide ([C(1)C(1)Im][Tf(2)N]) were deposited on differently terminated Ni(111) single crystal surfaces. The initial wetting behaviour, the growth characteristics, the molecular arrangement at the interface, and thermal reactivity were investigated using angle-resolved X-ray photoelectron spectroscopy (ARXPS). On clean Ni(111), the initial growth occurs in a layer-by-layer mode. At submonolayer coverages up to at least 0.40 ML, a preferential arrangement of the IL ions in a bilayer structure, with the imidazolium cations in contact with the Ni surface atoms and the anions on top of the cation, is deduced. For higher coverages, a transition to a checkerboard-type arrangement occurs, which is most likely due to repulsive dipole-dipole interactions in the first layer. An overall preference for a checkerboard-type adsorption behaviour, i.e., anions and cations adsorbing next to each other, is found on the oxygen-precovered O(√3×√3)R30° Ni(111) surface. The thermal stability of adsorbed IL layers on Ni(111) and on a fully oxidised Ni(111) surface was studied by heating the layers to elevated temperatures. For clean Ni(111) reversible adsorption takes place. For the oxidised surface, however, only cation-related moieties desorb, starting at ~450 K, while anion-related signals remain on the surface up to much higher temperatures.

Surface science and model catalysis with ionic liquid-modified materials.

Materials making use of thin ionic liquid (IL) films as support-modifying functional layer open up a variety of new possibilities in heterogeneous catalysis, which range from the tailoring of gas-surface interactions to the immobilization of molecularly defined reactive sites. The present report reviews recent progress towards an understanding of "supported ionic liquid phase (SILP)" and "solid catalysts with ionic liquid layer (SCILL)" materials at the microscopic level, using a surface science and model catalysis type of approach. Thin film IL systems can be prepared not only ex-situ, but also in-situ under ultrahigh vacuum (UHV) conditions using atomically well-defined surfaces as substrates, for example by physical vapor deposition (PVD). Due to their low vapor pressure, these systems can be studied in UHV using the full spectrum of surface science techniques. We discuss general strategies and considerations of this approach and exemplify the information available from complementary methods, specifically photoelectron spectroscopy and surface vibrational spectroscopy.

Liquid/solid interface of ultrathin ionic liquid films: [C1C1Im][Tf2N] and [C8C1Im][Tf2N] on Au(111).

Ultrathin films of two imidazolium-based ionic liquids (IL), [C(1)C(1)Im][Tf(2)N] (= 1,3-dimethylimidazolium bis(trifluoromethyl)imide) and [C(8)C(1)Im][Tf(2)N] (= 1-methyl-3-octylimidazolium bis(trifluoromethyl)imide) were prepared on a Au(111) single-crystal surface by physical vapor deposition in ultrahigh vacuum. The adsorption behavior, orientation, and growth were monitored via angle-resolved X-ray photoelectron spectroscopy (ARXPS). Coverage-dependent chemical shifts of the IL-derived core levels indicate that for both ILs the first layer is formed from anions and cations directly in contact with the Au surface in a checkerboard arrangement and that for [C(8)C(1)Im][Tf(2)N] a reorientation of the alkyl chain with increasing coverage is found. For both ILs, geometry models of the first adsorption layer are proposed. For higher coverages, both ILs grow in a layer-by-layer fashion up to thicknesses of at least 9 nm (>10 ML). Moreover, beam damage effects are discussed, which are mainly related to the decomposition of [Tf(2)N](-) anions directly adsorbed at the gold surface.

Density and surface tension of ionic liquids.

We measured the density and surface tension of 9 bis[(trifluoromethyl)sulfonyl]imide ([Tf(2)N](-))-based and 12 1-methyl-3-octylimidazolium ([C(8)C(1)Im](+))-based ionic liquids (ILs) with the vibrating tube and the pendant drop method, respectively. This comprehensive set of ILs was chosen to probe the influence of the cations and anions on density and surface tension. When the alkyl chain length in the [C(n)C(1)Im][Tf(2)N] series (n = 1, 2, 4, 6, 8, 10, 12) is increased, a decrease in density is observed. The surface tension initially also decreases but reaches a plateau for alkyl chain lengths greater than n = 8. Functionalizing the alkyl chains with ethylene glycol groups results in a higher density as well as a higher surface tension. For the dependence of density and surface tension on the chemical nature of the anion, relations are only found for subgroups of the studied ILs. Density and surface tension values are discussed with respect to intermolecular interactions and surface composition as determined by angle-resolved X-ray photoelectron spectroscopy (ARXPS). The absence of nonvolatile surface-active contaminants was proven by ARXPS.

Insights into the surface composition and enrichment effects of ionic liquids and ionic liquid mixtures.

A systematic study of ionic liquid surfaces by angle resolved X-ray photoelectron spectroscopy (ARXPS) is presented. By reviewing recent and presenting new results for imidazolium-based ionic liquids (ILs), we discuss the impact of chemical differences on surface composition and on surface enrichment effects. (1) For the hydrophilic ethylene glycol (EG) functionalised ILs [Me(EG)MIm][Tf(2)N], [Et(EG)(2)MIm][Tf(2)N] and [Me(EG)(3)MIm][Tf(2)N], which vary in the number of ethylene glycol units (from 1 to 3), we find that the surface composition of the near-surface region is in excellent agreement with the bulk composition, which is attributed to attractive interactions between the oxygen atoms on the cation to the hydrogen atoms on the imidazolium ring. (2) For [C(n)C(1)Im][Tf(2)N] (where n = 1-16), i.e. ILs with an alkyl chain of increasing length, an enrichment of the aliphatic carbons is observed for longer chains (n > 2), at the expense of the polar cation head groups and the anions in the first molecular layer, both of which are located approximately at the same distance from the outer surface. (3) To study the influence of the anion on the surface enrichment, we investigated ten ILs [C(8)C(1)Im][X] with the same cation, but very different anions [X](-). In all cases, surface enrichment of the cation alkyl chains is found, with the degree of enrichment decreasing with increasing size of the anion, i.e., it is most pronounced for the smallest anions and least pronounced for the largest anions. (4) For the IL mixture [C(2)C(1)Im][Tf(2)N] and [C(12)C(1)Im][Tf(2)N] we find a homogeneous distribution in the outermost surface region with no specific enrichment of the [C(12)C(1)Im](+) cation.

Functional nuclear organization of transcription and DNA replication: a topographical marriage between chromatin domains and the interchromatin compartment.

We studied the nuclear topography of RNA transcription and DNA replication in mammalian cell types with super-resolution fluorescence microscopy, which offers a resolution beyond the classical Abbe/Raleigh limit. Three-dimensional structured illumination microscopy (3D-SIM) demonstrated a network of channels and wider lacunas, called the interchromatin compartment (IC). The IC starts at nuclear pores and expands throughout the nuclear space. It is demarcated from the compact interior of higher-order chromatin domains (CDs) by a 100-200-nm thick layer of decondensed chromatin, termed the perichromatin region (PR). Nascent DNA, nascent RNA, RNA polymerase II (RNA Pol II), as well as histone modifications for transcriptionally competent/active chromatin, are highly enriched in the PR, whereas splicing speckles are observed in the interior of the IC. In line with previous electron microscopic evidence, spectral precision distance/position determination microscopy (SPDM) confirmed the presence of RNA Pol II clusters indicative of transcription factories. Still, a substantial part of transcription apparently takes place outside of such factories. Previous electron microscopic evidence has suggested that the functional nuclear organization of DNA replication depends on brownian movements of chromatin between the CD interior and the PR. As an incentive for future studies, we hypothesize that such movements also take place during transcription, i.e., only the actually transcribed part of a gene may be located within the PR, whereas its major part, including previously or later transcribed sequences, is embedded in a higher-order chromatin configuration in the interior of the CD.

Influence of different substituents on the surface composition of ionic liquids studied using ARXPS.

Angle resolved X-ray photoelectron spectroscopy has been used to study the surface composition of various nonfunctionalized and functionalized 1,3-dialkylimidazolium ionic liquids. For [CnC1Im][Tf2N] (where n = 2-16), an enrichment of the aliphatic carbon was observed for longer chains (n > or = 4). Enrichment of the aliphatic carbon also occurs for alkyl chains attached to the anion, as observed for [C2C1Im][OcOSO3]. Oligo(ethyleneglycol)ether (PEG) functionalities in the cation lead to a surface composition close to bulk stoichiometry and thus a loss in enrichment of the chains. This effect is attributed to attractive interactions between the oxygen atoms on the cation to the hydrogen atoms on the imidazolium ring for [Et(EG)2MIm] [Tf2N] and [Me(EG)3MIm][Tf2N].

A technical note on quantum dots for multi-color fluorescence in situ hybridization.

Quantum dots (Qdots) are semiconductor nanocrystals, which are photo-stable, show bright fluorescence with narrow, symmetric emission spectra and are available in multiple resolvable colors. We established a FISH protocol for the simultaneous visualization of up to 6 different DNA probes differentially labeled with Qdots and with conventional organic fluorochromes. Using a Leica SP5 laser scanning confocal microscope for image capture, we tested various combinations of hapten-labeled probes detected with streptavidin-Qdot525, sheep anti-digoxigenin-Qdot605, rat anti-dinitrophenyl-Qdot655 and goat anti-mouse-Qdot655, respectively, together with FITC-dUTP-, Cy3-dUTP- and Texas Red-dUTP-labeled probes. We further demonstrate that Qdots are suitable for imaging of FISH probes using 4Pi microscopy, which promises to push the resolution limits of light microscopy to 100 nanometers or less when applying a deconvolution algorithm, but requires the use of highly photo-stable fluors.

Influence of different anions on the surface composition of ionic liquids studied using ARXPS.

Angle-resolved X-ray photoelectron spectroscopy has been used to study the influence of different types of anions on the surface composition of ionic liquids (ILs). We have investigated nine ILs with the same cation, 1-octyl-3-methylimidazolium [C(8)C(1)Im](+), but very different anions. In all cases, an enrichment of the cation alkyl chains is found at the expense of the polar cation head groups and the anions in the first molecular layer. This enhancement effect decreases with increasing size of the anion, which means it is most pronounced for the smallest anions and least pronounced for the largest anions. A simple model is proposed to explain the experimental observations.

Chromosome shattering: a mitotic catastrophe due to chromosome condensation failure.

Chromosome shattering has been described as a special form of mitotic catastrophe, which occurs in cells with unrepaired DNA damage. The shattered chromosome phenotype was detected after application of a methanol/acetic acid (MAA) fixation protocol routinely used for the preparation of metaphase spreads. The corresponding phenotype in the living cell and the mechanism leading to this mitotic catastrophe have remained speculative so far. In the present study, we used V79 Chinese hamster cells, stably transfected with histone H2BmRFP for live-cell observations, and induced generalized chromosome shattering (GCS) by the synergistic effect of UV irradiation and caffeine posttreatment. We demonstrate that GCS can be derived from abnormal mitotic cells with a parachute-like chromatin configuration (PALCC) consisting of a bulky chromatin mass and extended chromatin fibers that tether centromeres at a remote, yet normally shaped spindle apparatus. This result hints at a chromosome condensation failure, yielding a "shattered" chromosome complement after MAA fixation. Live mitotic cells with PALCCs proceeded to interphase within a period similar to normal mitotic cells but did not divide. Instead they formed cells with highly abnormal nuclear configurations subject to apoptosis after several hours. We propose a factor depletion model where a limited pool of proteins is involved both in DNA repair and chromatin condensation. Chromosome condensation failure occurs when this pool becomes depleted.

Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls.

The vast majority of microscopic data in biology of the cell nucleus is currently collected using fluorescence microscopy, and most of these data are subsequently subjected to quantitative analysis. The analysis process unites a number of steps, from image acquisition to statistics, and at each of these steps decisions must be made that may crucially affect the conclusions of the whole study. This often presents a really serious problem because the researcher is typically a biologist, while the decisions to be taken require expertise in the fields of physics, computer image analysis, and statistics. The researcher has to choose between multiple options for data collection, numerous programs for preprocessing and processing of images, and a number of statistical approaches. Written for biologists, this article discusses some of the typical problems and errors that should be avoided. The article was prepared by a team uniting expertise in biology, microscopy, image analysis, and statistics. It considers the options a researcher has at the stages of data acquisition (choice of the microscope and acquisition settings), preprocessing (filtering, intensity normalization, deconvolution), image processing (radial distribution, clustering, co-localization, shape and orientation of objects), and statistical analysis.

Nonrigid registration of 3-d multichannel microscopy images of cell nuclei.

We present an intensity-based nonrigid registration approach for the normalization of 3-D multichannel microscopy images of cell nuclei. A main problem with cell nuclei images is that the intensity structure of different nuclei differs very much; thus, an intensity-based registration scheme cannot be used directly. Instead, we first perform a segmentation of the images from the cell nucleus channel, smooth the resulting images by a Gaussian filter, and then apply an intensity-based registration algorithm. The obtained transformation is applied to the images from the nucleus channel as well as to the images from the other channels. To improve the convergence rate of the algorithm, we propose an adaptive step length optimization scheme and also employ a multiresolution scheme. Our approach has been successfully applied using 2-D cell-like synthetic images, 3-D phantom images as well as 3-D multichannel microscopy images representing different chromosome territories and gene regions. We also describe an extension of our approach, which is applied for the registration of 3D + t (4-D) image series of moving cell nuclei.

DNA-repair protein distribution along the tracks of energetic ions.

A simple model of homogenous chromatin distribution in HeLa-cell nuclei suggests that the track of an energetic ion hits 30 nm chromatin fibers with a mean distance of 0.55 mum. To test this assumption, living HeLa-cells were irradiated at the irradiation setup of the ion microprobe SNAKE using the ion beams provided by the Munich 14 MV tandem accelerator. After irradiation, the distribution of 53BP1 protein foci was studied by immunofluorescence. The observed 53BP1 distribution along the tracks of 29 MeV (7)Li ions and 24 MeV (12)C ions differed significantly from the expectations resulting from the simple chromatin model, suggesting that the biological track structure is determined by cell nuclear architecture with higher order organisation of chromatin.

Towards many colors in FISH on 3D-preserved interphase nuclei.

The article reviews the existing methods of multicolor FISH on nuclear targets, first of all, interphase chromosomes. FISH proper and image acquisition are considered as two related components of a single process. We discuss (1) M-FISH (combinatorial labeling + deconvolution + wide-field microscopy); (2) multicolor labeling + SIM (structured illumination microscopy); (3) the standard approach to multicolor FISH + CLSM (confocal laser scanning microscopy; one fluorochrome - one color channel); (4) combinatorial labeling + CLSM; (5) non-combinatorial labeling + CLSM + linear unmixing. Two related issues, deconvolution of images acquired with CLSM and correction of data for chromatic Z-shift, are also discussed. All methods are illustrated with practical examples. Finally, several rules of thumb helping to choose an optimal labeling + microscopy combination for the planned experiment are suggested.

Rise, fall and resurrection of chromosome territories: a historical perspective. Part II. Fall and resurrection of chromosome territories during the 1950s to 1980s. Part III. Chromosome territories and the functional nuclear architecture: experiments and models from the 1990s to the present.

Part II of this historical review on the progress of nuclear architecture studies points out why the original hypothesis of chromosome territories from Carl Rabl and Theodor Boveri (described in part I) was abandoned during the 1950s and finally proven by compelling evidence forwarded by laser-uv-microbeam studies and in situ hybridization experiments. Part II also includes a section on the development of advanced light microscopic techniques breaking the classical Abbe limit written for readers with little knowledge about the present state of the theory of light microscopic resolution. These developments have made it possible to perform 3D distance measurements between genes or other specifically stained, nuclear structures with high precision at the nanometer scale. Moreover, it has become possible to record full images from fluorescent structures and perform quantitative measurements of their shapes and volumes at a level of resolution that until recently could only be achieved by electron microscopy. In part III we review the development of experiments and models of nuclear architecture since the 1990s. Emphasis is laid on the still strongly conflicting views about the basic principles of higher order chromatin organization. A concluding section explains what needs to be done to resolve these conflicts and to come closer to the final goal of all studies of the nuclear architecture, namely to understand the implications of nuclear architecture for nuclear functions.

Transition from initiation to promoter proximal pausing requires the CTD of RNA polymerase II.

The C-terminal domain (CTD) of mammalian RNA polymerase II consists of 52 repeats of the consensus hepta-peptide YSPTSPS, and links transcription to the processing of pre-mRNA. Although Pol II with a CTD shortened to five repeats (Pol II Delta5) is transcriptionally inactive on chromatin templates, it is not clear whether CTD is required for promoter recognition in vivo. Here, we demonstrate that in the context of chromatin, Pol II Delta5 can bind to the c-myc promoter with the same efficiency as wild type Pol II. However, Pol II Delta5 does not form a stable initiation complex, and does not transcribe promoter proximal sequences. Fluorescence recovery after photobleaching (FRAP) experiments with cells expressing enhanced green fluorescent protein (EGFP)-tagged Delta5 or wildtype Pol II revealed a single, highly mobile Pol II Delta5 fraction whereas wildtype Pol II yielded less mobile fractions. These data suggest that CTD is not required for promoter recognition, but rather for subsequent formation of a stable initiation complex and isomerization to an elongation competent complex.

Three dimensional analysis of histone methylation patterns in normal and tumor cell nuclei.

Histone modifications represent an important epigenetic mechanism for the organization of higher order chromatin structure and gene regulation. Methylation of position-specific lysine residues in the histone H3 and H4 amino termini has linked with the formation of constitutive and facultative heterochromatin as well as with specifically repressed single gene loci. Using an antibody, directed against dimethylated lysine 9 of histone H3 and several other lysine methylation sites, we visualized the nuclear distribution pattern of chromatin flagged by these methylated lysines in 3D preserved nuclei of normal and malignant cell types. Optical confocal serial sections were used for a quantitative evaluation. We demonstrate distinct differences of these histone methylation patterns among nuclei of different cell types after exit of the cell cycle. Changes in the pattern formation were also observed during the cell cycle. Our data suggest an important role of methylated histones in the reestablishment of higher order chromatin arrangements during telophase/early G1. Cell type specific histone methylation patterns are possibly casually involved in the formation of cell type specific heterochromatin compartments, composed of (peri)centromeric regions and chromosomal subregions from neighboring chromosomes territories, which contain silent genes.

Microirradiation of cells with energetic heavy ions.

The ion microprobe SNAKE at the Munich 14 MV tandem accelerator achieves beam focussing by a superconducting quadrupole doublet and can make use of a broad range of ions and ion energies, from 20 MeV protons to 200 MeV gold ions. Because of these properties, SNAKE is particularly attractive for biological microbeam experiments. Here we describe the adaptation of SNAKE for microirradiation of cell samples. This includes enlarging of the focal distance in order to adjust the focal plane to the specimen stage of a microscope, construction of a beam exit window in a flexible nozzle and of a suitable cell containment, as well as development of procedures for on-line focussing of the beam, preparation of single ions and scanning by electrostatic deflection of the beam. When irradiating with single 100 MeV (16)O ions, the adapted set-up permits an irradiation accuracy of 0.91 microm (full width at half maximum) in the x-direction and 1.60 microm in the y-direction, as demonstrated by retrospective track etching of polycarbonate foils. Accumulation of the repair protein Rad51, as detected by immunofluorescence, was used as a biological track detector after irradiation of HeLa cells with geometric patterns of counted ions. Observed patterns of fluorescence foci agreed reasonably well with irradiation patterns, indicating successful adaptation of SNAKE. In spite of single ion irradiation, we frequently observed split fluorescence foci which might be explained by small-scale chromatin movements.