Comparative analysis of topographic distribution of acetylated histone H4 by using confocal microscopy and a deconvolution system

Chromosomics: Bridging the Gap between Genomes and Chromosomes

The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.

Development of a quantitative pachytene chromosome map and its unification with somatic chromosome and linkage maps of rice (Oryza sativa L.)

A quantitative pachytene chromosome map of rice (Oryza sativa L.) was developed using imaging methods. The map depicts not only distribution patterns of chromomeres specific to pachytene chromosomes, but also the higher order information of chromosomal structures, such as heterochromatin (condensed regions), euchromatin (decondensed regions), the primary constrictions (centromeres), and the secondary constriction (nucleolar organizing regions, NOR). These features were image analyzed and quantitatively mapped onto the map by Chromosome Image Analyzing System ver. 4.0 (CHIAS IV). Correlation between H3K9me2, an epigenetic marker and formation and/or maintenance of heterochromatin, thus was, clearly visualized. Then the pachytene chromosome map was unified with the existing somatic chromosome and linkage maps by physically mapping common DNA markers among them, such as a rice A genome specific tandem repeat sequence (TrsA), 5S and 45S ribosomal RNA genes, five bacterial artificial chromosome (BAC) clones, four P1 bacteriophage artificial chromosome (PAC) clones using multicolor fluorescence in situ hybridization (FISH). Detailed comparison between the locations of the DNA probes on the pachytene chromosomes using multicolor FISH, and the linkage map enabled determination of the chromosome number and short/long arms of individual pachytene chromosomes using the chromosome number and arm assignment designated for the linkage map. As a result, the quantitative pachytene chromosome map was unified with two other major rice chromosome maps representing somatic prometaphase chromosomes and genetic linkages. In conclusion, the unification of the three rice maps serves as an indispensable basic information, not only for an in-depth comparison between genetic and chromosomal data, but also for practical breeding programs.

Cooperative synthesis of dopamine by non-dopaminergic neurons as a compensatory mechanism in the striatum of mice with MPTP-induced Parkinsonism

Since the late 80s it has been repeatedly shown that besides dopaminergic neurons, the brain contains so-called monoenzymatic neurons possessing one of the enzymes of dopamine (DA) synthesis, tyrosine hydroxylase (TH) or aromatic l-amino acid decarboxylase (AADC). However, the data on the existence of monoenzymatic neurons in the striatum remain controversial, and little is known about their functional significance. The aim of this study was to test our hypothesis that monoenzymatic TH-containing neurons produce DA in cooperation with the neurons containing AADC, which might help to compensate DA deficiency under the failure of the nigrostriatal dopaminergic system. Using a combination of techniques: retrograde tracing, qPCR and immunolabeling for TH, AADC and MAP2, we showed that the striatum of mice with normal and degraded dopaminergic system comprises of monoenzymatic TH- and AADC-containing neurons. To provide evidence for cooperative synthesis of DA, we used an ex vivo model of inhibiting of DA synthesis by blocking transport of l-DOPA, produced in monoenzymatic TH-containing neurons, to neurons containing AADC by means of l-leucine, a competitive inhibitor of the membrane transporter of large neutral amino acids, and l-DOPA. With this original approach, cooperative synthesis of DA in the striatum was proven in MPTP-treated mice but not in the control. Furthermore, we demonstrated that the proportion of DA produced through cooperative synthesis in the striatum of MPTP-treated mice increases as the degradation of dopaminergic system proceeds. An increase in the proportion of cooperative synthesis of DA alongside degradation of the dopaminergic system is also proved by an increase of both TH gene expression and the number of TH-immunoreactive structures in the striatum. Thus, these data suggest that the cooperative synthesis of DA in the degraded striatum is an up-regulated compensatory reaction, which plays an increasing role as DA deficiency rises, and might be considered among the principal mechanisms of neuroplasticity in neurodegenerative diseases.

Chapter 5: Imaging in depth: controversies and opportunities

One enduring challenge of biological imaging is achieving depth of penetration-into cells, tissues, and animals. How deeply can we probe and with what resolution and efficacy? These are critical issues as microscopists seek to push ever deeper, while resolving structural details and observing specific molecular events. In this guide to depth-appropriate modalities, standard optical platforms such as confocal and two-photon microscopes are considered along with complementary imaging modalities that range in depth of penetration. After an introduction to basic techniques, the trade-offs and limitations that distinguish competing technologies are considered, with emphasis on the visualization of subcellular structures and dynamic events. Not surprisingly, there are differences of opinion regarding imaging technologies, as highlighted in a section on point-scanning and Nipkow-disk style confocal microscopes. Confocal microscopy is then contrasted with deconvolution and multi-photon imaging modalities. It is also important to consider the detectors used by current instruments (such as PMTs and CCD cameras). Ultimately specimen properties, in conjunction with instrumentation, determine the depth at which subcellular operations and larger-scale biological processes can be visualized. Relative advantages are mentioned in the context of experiment planning and instrument-purchase decisions. Given the rate at which new optical techniques are being invented, this report should be viewed as a snapshot of current capabilities, with the goal of providing a framework for thinking about new developments.

Comprehensive analysis of dynamics of histone H4 acetylation in mitotic barley cells

Nucleosomal histones are covalently modified at specific amino acid residues. In the case of histone H4, four lysines (K5, K8, K12, and K16) are acetylated. In the current studies, we examined the dynamics of histone H4 acetylation at K8 and K12 in mitotic barley cells using a three-dimensional immunofluorescent method. Based on the results and previous studies on the dynamics of K5 and K16 acetylation, we provide a comprehensive view of the dynamics of H4 acetylation. Interphase nuclei exhibit strong acetylation in the centromeric region at K5, K8 and K12. In the case of K12, strong acetylation at nucleolar organizing regions was observed from prophase to anaphase. The dynamics of K12 were closely related to those of K5. On the other hand, K8 exhibited a pattern of almost uniform acetylation from prophase to telophase and strong acetylation in distal regions of chromosomes at both metaphase and anaphase, which is very similar to the dynamics of K16 acetylation. Thus, it appears that there is pair-wise acetylation of K12 and K5 in the nucleolar organizing regions and of K8 and K16 in the gene-rich regions. Together, these results suggest that pair-wise dynamics of H4 acetylation regulate chromosomal structure and function during the cell cycle.

An upper limit of the ratio of DNA volume to nuclear volume exists in plants

The variations in nuclear DNA content from 2 x 10(2) to 2.5 x 10(5) Mbp are reported in higher plants. The major finding so far is that the genome size of plant species differs by three orders of magnitude, which are more variable than the other organisms. Investigations pertaining to the manner in which DNA is packaged in the nucleus provide us with basic information on the made of DNA existence in the plant nucleus. However, the fundamentals on nuclear DNA content and nuclear size, which underlie and enable the flexible containment of such large differences in nuclear DNA content, remain unknown. We analyzed the nuclear volumes of plants with 2C value DNA contents ranging from 3.2 x 10(2) to 1.0 x 10(5) Mbp. As a result, we obtained a constant ratio between the DNA volume and nuclear volume, which does not exceed 3%. Furthermore, we also demonstrate that the nuclear Rabl model of chromatin organisation is not a common 3-D structure, even in plants with large nuclear DNA contents. The existence of an upper limit of DNA volume ratio would present a basal parameter for the future insight into the nuclear organisation in higher plants.

Neurons possessing enzymes of dopamine synthesis in the mediobasal hypothalamus of rats. Topographic relations and axonal projections to the median eminence in ontogenesis

We evaluated the topographic relations between tyrosine hydroxylase (TH)- and/or aromatic L-amino acid decarboxylase (AADC)-immunoreactive neurons in the arcuate nucleus (AN), as well as between TH- and/or AADC-immunoreactive axons in the median eminence (ME) in rats at the 21st embryonic day, 9th postnatal day, and in adulthood. The double-immunofluorescent technique in combination with confocal microscopy was used. Occasional bienzymatic neurons but numerous monoenzymatic TH- or AADC-immunoreactive neurons were observed in fetuses. There was almost no overlap in the distribution of monoenzymatic neurons, and therefore few appositions were observed in between. In postnatal animals, numerous bienzymatic neurons appeared in addition to monoenzymatic neurons. They were distributed throughout the AN resulting in the increased frequency of appositions. Furthermore, specialized-like contacts between monoenzymatic TH- and AADC-immunoreactive neurons appeared. The quantification of the fibers in the ME showed that there were large specific areas of the monoenzymatic TH-immunoreactive fibers and bienzymatic fibers in fetuses, followed by the gradual reduction of the former and the increase of the latter to adulthood. The specific area of the monoenzymatic AADC-immunoreactive fibers in fetuses was rather low, and thereafter increased progressively to adulthood. The fibers of all the types were in apposition in the ME at each studied age. Close topographic relations between the neurons containing individual complementary enzymes of dopamine synthesis at the level of cell bodies and axons suggest functional interaction in between.

Short communication: the cell cycle dependent phosphorylation of histone H3 is correlated with the condensation of plant mitotic chromosomes

Mitotically dividing cells of Secale cereale, Hordeum vulgare and Vicia faba were studied by indirect immunofluorescence using an antibody recognizing phosphorylated histone H3. The study revealed the following features: (i) the H3 phosphorylation starts at prophase and ends at telophase in the pericentromeric chromatin, is associated with the condensation of mitotic chromosomes and is independent of the distribution of late replicating heterochromatin. (ii) Compared with other chromosome regions, the pericentromeric chromatin is histone H3 hyperphos- phorylated. (iii) The study of a semi-dicentric chromo- some revealed that only at intact centromeres is the chromatin hyperphosphorylated at H3.