Rise, fall and resurrection of chromosome territories: a historical perspective. Part I. The rise of chromosome territories

It is now generally accepted that chromosomes in the cell nucleus are organized in distinct domains, first called chromosome territories in 1909 by the great cytologist Theodor Boveri. Yet, even today chromosomes have remained enigmatic individuals, whose structures, arrangements and functions in cycling and post-mitotic cells still need to be explored in full detail. Whereas numerous recent reviews describe present evidence for a dynamic architecture of chromosome territories and discuss the potential significance within the functional compartmentalization of the nucleus, a comprehensive historical account of this important concept of nuclear organization was lacking so far. Here, we describe the early rise of chromosome territories within the context of the discovery of chromosomes and their fundamental role in heredity, covering a period from the 1870th to the early 20th century (part I, this volume). In part II (next volume) we review the abandonment of the chromosome territory concept during the 1950th to 1980th and the compelling evidence, which led to its resurrection during the 1970th to 1980th.     

Association of chromosome territories with the nuclear matrix. Disruption of human chromosome territories correlates with the release of a subset of nuclear matrix proteins.

To study the possible role of the nuclear matrix in chromosome territory organization, normal human fibroblast cells are treated in situ via classic isolation procedures for nuclear matrix in the absence of nuclease (e.g., DNase I) digestion, followed by chromosome painting. We report for the first time that chromosome territories are maintained intact on the nuclear matrix. In contrast, complete extraction of the internal nuclear matrix components with RNase treatment followed by 2 M NaCl results in the disruption of higher order chromosome territory architecture. Correlative with territorial disruption is the formation of a faint DNA halo surrounding the nuclear lamina and a dispersive effect on the characteristically discrete DNA replication sites in the nuclear interior. Identical results were obtained using eight different human chromosome paints. Based on these findings, we developed a fractionation strategy to release the bulk of nuclear matrix proteins under conditions where the chromosome territories are maintained intact. A second treatment results in disruption of the chromosome territories in conjunction with the release of a small subset of acidic proteins. These proteins are distinct from the major nuclear matrix proteins and may be involved in mediating chromosome territory organization.     

Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications

In the nucleus of animal and plant cells individual chromosomes maintain a compartmentalized structure. Chromosome territories (CTs), as these structures were named by Theodor Boveri, are essential components of the higher-order chromatin architecture. Recent studies in mammals and non-mammalian vertebrates indicate that the radial position of a given CT (or segments thereof) is correlated with its size, its gene-density and its replication timing. As a representative case, chicken cell nuclei show highly consistent radial chromatin arrangements: gene-rich, early replicating microchromosomes are clustered within the nuclear interior, while gene-poor, later replicating macrochromosomes are preferentially located at the nuclear periphery. In humans, chromosomes 18 and 19 (HSA18 and 19) territories that are of similar size show a distinctly different position in the cell nuclei of lymphocytes and lymphoblastoid cells: the gene-rich and early replicating HSA19 CTs are typically found close to the nuclear center, while the gene-poor and later replicating HSA18 CTs are preferentially located at the nuclear periphery. Recent comparative maps between human and chicken chromosomes revealed that the chicken macrochromosomes 2 and Z contain the genes homologous to HSA18, while the genes on HSA19 are located onto the chicken microchromosomes. These data lend tentative support to the hypothesis that differences in the radial nuclear positions of gene-rich, early replicating and gene-poor, later replicating chromatin have been evolutionarily conserved during a period of more than 300 million years irrespective of the evolution of highly divergent karyotypes between humans and chicken.     

Der Zellkern – eine Stadt in der Zelle,Teil 2

The Cell Nucleus – A Town in the Cell. Part II: Chromatin Nanoarchitecture and Gene Regulation In the second part of this article on nuclear architecture we describe the ground‐breaking potential of super‐resolution fluorescence microscopy (nanoscopy) and new molecular approaches to study the structure of chromatin domains at the nanometer scale and explore their 3D positions in larger chromatin domain clusters. New results and models argue for a decisive role of these structures in nuclear functions, such as gene regulation.     

Uncertainty in life cycle costing for long-range infrastructure. Part II: guidance and suitability of applied methods to address uncertainty

Life cycle costing (LCC) is the state-of-the-art method to economically evaluate long-term projects over their life spans. However, uncertainty in long-range planning raises concerns about LCC results. In Part I of this series, we developed a holistic framework of the different types of uncertainty in infrastructure LCCs. We also collected methods to address these uncertainties. The aim of Part II is to evaluate the suitability of methods to cope with uncertainty in LCC. Part I addressed two research gaps. It presented a systematic collection of uncertainties and methods in LCC and, furthermore, provided a holistic categorization of both. However, Part I also raised new issues. First, a combined analysis of sources and methods is still outstanding. Such an investigation would reveal the suitability of different methods to address a certain type of uncertainty. Second, what has not been assessed so far is what types of uncertainty are insufficiently addressed in LCC. This would be a feature to improve accuracy of LCC results within LCC, by suggesting options to better cope with uncertainty. To address these research gaps, we conducted a systematic literature review. Part II analyzed the suitability of methods to address uncertainties. The suitability depends on data availability, type of data (tangible, intangible, random, non-random), screened hotspots, and tested modeling specifications. We identified types of uncertainties and methods that have been insufficiently addressed. The methods include probabilistic modeling such as design of experiment or subset simulation and evolutionary algorithm and Bayesian modeling such as the Bayesian latent Markov decision process. Subsequently, we evaluated learning potential from other life cycle assessment (LCA) and life cycle sustainability assessment (LCSA). This analysis revealed 28 possible applications that have not yet been used in LCC. Lastly, we developed best practices for LCC practitioners. This systematic review complements prior research on uncertainty in LCC for infrastructure, as laid out in Part I. Part II concludes that all relevant methods to address uncertainty are currently applied in LCC. Yet, the level of application is different. Moreover, not all methods are equally suited to address different categories of uncertainty. This review offers guidance on what to do for each source and type of uncertainty. It illustrates how methods can address both based on current practice in LCC, LCA, and LCSA. The findings of Part II encourage a dialog between practitioners of LCC, LCA, and LCSA to advance research and practice in uncertainty analysis.     

An examination of the phenol-croton oil peel: Part III. The plastic surgeons' role

In Part II, the author focused on the lay peelers' history and success using croton oil-containing phenol peeling recipes. In Part III, the author reviews what was known or should have been known about croton oil and phenol as physicians became keenly interested in face peeling in the mid-1950s. The lay peelers recognized that croton oil was a critical ingredient of the so-called phenol peel while physicians focused on phenol without recognizing the intense cytotoxic effect of croton resin. Physicians have persisted in this systematic error for 40 years. Both dermatology and plastic surgery have shown a remarkable credulity about phenol's action and lack of curiosity about croton oil's action. A hitherto unreferenced and unknown croton oil-containing formula of Adolph Brown, patented in 1959, has been unearthed, preceding Litton's and Baker's formulas in time. The recollections of Litton, Baker, Truppman, and Georgiade shed some light on the interaction between them and the lay peelers and how the formulas were transferred. Other plastic surgeons probably acquired the same knowledge, used it in their practices, but chose not to draw attention to it. None of the physicians credited the lay peelers. Brown, Litton, and Baker each could have published a complete formula, but only Baker did. However, his formula was vastly stronger than the lay formulas but, nevertheless, came to dominate medical peeling for the next 35 years because of its simplicity of preparation. A review of the peel literature reveals many oft-repeated but unsupported dogmas regarding the mode of action of phenol, which have obscured our understanding of the phenol-croton oil peel. Animal studies exist that refute these dogmas, e.g., (1) lesser concentrations of phenol wound more deeply; and (2) phenol has an all-or-nothing action. As well, studies from the early 1980s showed that the presence of croton oil caused much deeper burns than phenol alone. Suggested areas of research that could solve the conundrum of the phenol-croton oil peel are presented.     

Chloroplast structure: from chlorophyll granules to supra-molecular architecture of thylakoid membranes

This review provides a brief historical account of how microscopical studies of chloroplasts have contributed to our current knowledge of the structural and functional organization of thylakoid membranes. It starts by tracing the origins of the terms plastid, grana, stroma and chloroplasts to light microscopic studies of 19th century German botanists, and then describes how different types of electron microscopical techniques have added to this field. The most notable contributions of thin section electron microscopy include the elucidation of the 3-D organization of thylakoid membranes, the discovery of prolamellar bodies in etioplasts, and the structural changes in thylakoid architecture that accompany the light-dependent transformation of etioplasts into chloroplasts. Attention is then focused on the roles that freeze-fracture and freeze-etch electron microscopy and immuno electron microscopy have played in defining the extent to which the functional complexes of thylakoids are non-randomly distributed between appressed, grana and non-appressed stroma thylakoids. Studies reporting on how this lateral differentiation can be altered experimentally, and how the spatial organization of functional complexes is affected by alterations in the light environment of plants are also included in this discussion. Finally, the review points to the possible uses of electron microscope tomography techniques in future structural studies of thylakoid membranes. This revised version was published online in August 2006 with corrections to the Cover Date.     

Mitosis in Barbulanympha. I. Spindle structure, formation, and kinetochore engagement

Successful culture of the obligatorily anaerobic symbionts residing in the hindgut of the wood-eating cockroach Cryptocercus punctulatus now permits continuous observation of mitosis in individual Barbulanympha cells. In Part I of this two-part paper, we report methods for culture of the protozoa, preparation of microscope slide cultures in which Barbulanympha survived and divided for up to 3 days, and an optical arrangement which permits observation and through-focus photographic recording of dividing cells, sequentially in differential interference contrast and rectified polarized light microscopy. We describe the following prophase events and structures: development of the astral rays and large extranuclear central spindle from the tips of the elongate-centrioles; the fine structure of spindle fibers and astral rays which were deduced in vivo from polarized light microscopy and seen as a particular array of microtubules in thin-section electron micrographs; formation of chromosomal spindle fibers by dynamic engagement of astral rays to the kinetochores embedded in the persistent nuclear envelope; and repetitive shortening of chromosomal spindle fibers which appear to hoist the nucleus to the spindle surface, cyclically jostle the kinetochores within the nuclear envelope, and churn the prophase chromosomes. The observations described here and in Part II have implications both for the evolution of mitosis and for understanding the mitotic process generally.     

Receptor-mediated tumor targeting with radiopeptides. Part 1. General concepts and methods: applications to somatostatin receptor-expressing tumors

Radiolabeled peptides have become important tools in nuclear oncology, both as diagnostics and more recently also as therapeutics. They represent a distinct sector of the molecular targeting approach, which in many areas of therapy will implement the old "magic bullet" concept by specifically directing the therapeutic agent to the site of action. In this three-part review, we present a comprehensive overview of the literature on receptor-mediated tumor targeting with the different radiopeptides currently studied. Part I summarizes the general concepts and methods of targeting, the selection of radioisotopes, chelators, and the criteria of peptide ligand development. Then, the >400 studies on the application to somatostatin/somatostatin-release inhibiting factor receptor-mediated tumor localization and treatment will be reviewed, demonstrating that peptide radiopharmaceuticals have gained an important position in clinical medicine.     

Receptor-Mediated Tumor Targeting with Radiopeptides. Part 1. General Concepts and Methods: Applications to Somatostatin Receptor-Expressing Tumors

Radiolabeled peptides have become important tools in nuclear oncology, both as diagnostics and more recently also as therapeutics. They represent a distinct sector of the molecular targeting approach, which in many areas of therapy will implement the old “magic bullet” concept by specifically directing the therapeutic agent to the site of action. In this three-part review, we present a comprehensive overview of the literature on receptor-mediated tumor targeting with the different radiopeptides currently studied. Part I summarizes the general concepts and methods of targeting, the selection of radioisotopes, chelators, and the criteria of peptide ligand development. Then, the >400 studies on the application to somatostatin/somatostatin-release inhibiting factor receptor-mediated tumor localization and treatment will be reviewed, demonstrating that peptide radiopharmaceuticals have gained an important position in clinical medicine.     

Light scattering vs. microscopy for measuring average cell size and shape.

Light-scattering photometry is compared with electron and light microscopy as a source of information about the average size and shape of cells in population. Examined are the effects of limited instrument resolution, necessary experimental procedures, and cell heterogeneity. Information theory is used to survey the relative amounts of information provided by photometric and microscopic measurements. Then in model exploratory experiments, cell size and shape and changes therein are determined both by microscopy and by photometry for spherical and spheroidal cells. Scattering theory is used to calculate photometrically observed light from cell parameters. It is found that if certain other appropriate information about the morphological property of interest is available, then visible light photometry is the preferred method for obtaining quantitative information. It has good absolute sensitivity (0.01-0.10 micrometers resolution), its results are relatively unaffected by sample heterogeneity, it is nondestructive and compatible with many other techniques, it requires no sample preparation, and it provides its information in real time.     

Congenital Anomalies of the Limbs: Part II. Psychological and Educational Aspects

As a preparatory step towards the development of a complete habilitation program for children with congenital limb anomalies associated with maternal ingestion of thalidomide, the medical records of all patients with congenital limb anomalies referred to the Rehabilitation Institute of Montreal in the past decade were studied, and an examination and a thorough reassessment were made of 41 patients (21 males and 20 females). The medical and prosthetic aspects were dealt with in Part I of this paper. Part II describes, in a joint report, the results of psychiatric, psychological and educational assessments.There was no evidence of major emotional disorder in any of the patients, although conflicts were intensified by the presence of the physical anomaly. No relation was found between intelligence, emotional adjustment and disability. The patient''s attitude towards his disability and prosthesis is definitely influenced by the degree of parental acceptance of the handicap and by the character of the emotional undertones in the total environment. In order to favour the occurrence of the healthiest modes of development in these children, the authors believe that the medical profession should be made fully aware of the physical and emotional problems which may arise after the birth of a deformed child. It is considered very important that the mother should receive psychotherapeutic support as soon as possible after the child is born.     

Structure and dynamics of human interphase chromosome territories in vivo

A new approach is presented which allows the in vivo visualization of individual chromosome territories in the nuclei of living human cells. The fluorescent thymidine analog Cy3-AP3-dUTP was microinjected into the nuclei of cultured human cells, such as human diploid fibroblasts, HeLa cells and neuroblastoma cells. The fluorescent analog was incorporated during S-phase into the replicating genomic DNA. Labelled cells were further cultivated for several cell cycles in normal medium. This well-known scheme yielded sister chromatid labelling. Random segregation of labelled and unlabelled chromatids into daughter nuclei resulted in nuclei exhibiting individual in vivo detectable chromatid territories. The territories were composed of subcompartments with diameters ranging between approximately 400 and 800 nm which we refer to as subchromosomal foci. Time-resolved in vivo studies demonstrated changes of positioning and shape of territories and subchromosomal foci. The hypothesis that subchromosomal foci persist as functionally distinct entities was supported by double labelling of chromatin with CldU and IdU, respectively, at early and late S-phase and subsequent cultivation of corresponding cells for 5–10 cell cycles before fixation and immunocytochemical detection. This scheme yielded segregated chromatid territories with distinctly separated subchromosomal foci composed of either early- or late-replicating chromatin. The size range of subchromosomal foci was similar after shorter (2 h) and longer (16 h) labelling periods and was observed in nuclei of both living and fixed cells, suggesting their structural identity. A possible functional relevance of chromosome territory compartmentalization into subchromosomal foci is discussed in the context of present models of interphase chromosome and nuclear architecture. Received: 10 November 1997 / Accepted: 24 November 1997     

Helicase mechanisms and the coupling of helicases within macromolecular machines. Part I: Structures and properties of isolated helicases

Helicases are proteins that harness the chemical free energy of ATP hydrolysis to catalyze the unwinding of double-stranded nucleic acids. These enzymes have been much studied in isolation, and here we review what is known about the mechanisms of the unwinding process. We begin by considering the thermally driven 'breathing' of double-stranded nucleic acids by themselves, in order to ask whether helicases might take advantage of some of these breathing modes. We next provide a brief summary of helicase mechanisms that have been elucidated by biochemical, thermodynamic, and kinetic studies, and then review in detail recent structural studies of helicases in isolation, in order to correlate structural findings with biophysical and biochemical results. We conclude that there are certainly common mechanistic themes for helicase function, but that different helicases have devised solutions to the nucleic acid unwinding problem that differ in structural detail. In Part II of this review (to be published in the next issue of this journal) we consider how these mechanisms are further modified to reflect the functional coupling of these proteins into macromolecular machines, and discuss the role of helicases in several central biological processes to illustrate how this coupling actually works in the various processes of gene expression.     

Cannabidiol: an overview of some chemical and pharmacological aspects. Part I: chemical aspects

Over the last few years considerable attention has focused on cannabidiol (CBD), a major non-psychotropic constituent of Cannabis. In Part I of this review we present a condensed survey of the chemistry of CBD; in Part II, to be published later, we shall discuss the anti-convulsive, anti-anxiety, anti-psychotic, anti-nausea and anti-rheumatoid arthritic properties of CBD. CBD does not bind to the known cannabinoid receptors and its mechanism of action is yet unknown. In Part II we shall also present evidence that it is conceivable that, in part at least, its effects are due to its recently discovered inhibition of anandamide uptake and hydrolysis and to its anti-oxidative effect.     

3D analysis of chromosome architecture: advantages and limitations with SEM

Three-dimensional mitotic plant chromosome architecture can be investigated with the highest resolution with scanning electron microscopy compared to other microscopic techniques at present. Specific chromatin staining techniques making use of simultaneous detection of back-scattered electrons and secondary electrons have provided conclusive information on the distribution of DNA and protein in barley chromosomes through mitosis. Applied to investigate the structural effects of different preparative procedures, these techniques were the groundwork for the "dynamic matrix model" for chromosome condensation, which postulates an energy-dependent process of looping and bunching of chromatin coupled with attachment to a dynamic matrix of associated protein fibers. Data from SEM analysis shows basic higher order chromatin structures: chromomeres and matrix fibers. Visualization of nanogold-labeled phosphorylated histone H3 (ser10) with high resolution on chromomeres shows that functional modifications of chromatin can be located on structural elements in a 3D context.     

Epstein-Barr virus BGLF4 kinase induces premature chromosome condensation through activation of condensin and topoisomerase II

Previous studies of Epstein-Barr virus (EBV) replication focused mainly on the viral and cellular factors involved in replication compartment assembly and controlling the cell cycle. However, little is known about how EBV reorganizes nuclear architecture and the chromatin territories. In EBV-positive nasopharyngeal carcinoma NA cells or Akata cells, we noticed that cellular chromatin becomes highly condensed upon EBV reactivation. In searching for the possible mechanisms involved, we found that transient expression of EBV BGLF4 kinase induces unscheduled chromosome condensation, nuclear lamina disassembly, and stress fiber rearrangements, independently of cellular DNA replication and Cdc2 activity. BGLF4 interacts with condensin complexes, the major components in mitotic chromosome assembly, and induces condensin phosphorylation at Cdc2 consensus motifs. BGLF4 also stimulates the decatenation activity of topoisomerase II, suggesting that it may induce chromosome condensation through condensin and topoisomerase II activation. The ability to induce chromosome condensation is conserved in another gammaherpesvirus kinase, murine herpesvirus 68 ORF36. Together, these findings suggest a novel mechanism by which gammaherpesvirus kinases may induce multiple premature mitotic events to provide more extrachromosomal space for viral DNA replication and successful egress of nucleocapsid from the nucleus.