Higher levels of organization in chromosomes

Karyotype heterogeneity and unclassified chromosomal abnormalities

In a departure from traditional gene-centric thinking with regard to cytogenetics and cytogenomics, the recently introduced genome theory calls upon a re-focusing of our attention on karyotype analyses of disease conditions. Karyotype heterogeneity has been demonstrated to be directly involved in the somatic cell evolution process which is the basis of many common and complex diseases such as cancer. To correctly use karyotype heterogeneity and apply it to monitor system instability, we need to include many seemingly unimportant non-specific chromosomal aberrations into our analysis. Traditionally, cytogenetic analysis has been focused on identifying recurrent types of abnormalities, particularly those that have been linked to specific diseases. In this perspective, drawing on the new framework of 4D-genomics, we will briefly review the importance of studying karyotype heterogeneity. We have also listed a number of overlooked chromosomal aberrations including defective mitotic figures, chromosome fragmentation as well as genome chaos. Finally, we call for the systematic discovery/characterization and classification of karyotype abnormalities in human diseases, as karyotype heterogeneity is the common factor that is essential for somatic cell evolution.

Interrelationships among major protistan groups based on a parsimony network of 5S rRNA sequences

To test the validity of the maximum parsimony approach to discern protistan interrelationships, we have derived an optimal network of 16S-like rRNA sequences using our parsimony algorithm and compared it with those reported using the distance matrix method. We have also derived an optimal network topology of 50 5S rRNA sequences through an interactive search using our algorithm. In both these networks, the kinetoplastids and euglenoids form a linkage group with Dictyostelium emerging from its neighbourhood. The cryptophytes, dinoflagellates and chromophytes and green algae emerge as independent lines suggesting that plastids arose more than once during protistan evolution. The large 5S rRNA tree further indicates independent origins of mesozoa and metazoa; kinetoplastids and ciliates; and diphyletic origin of fungi. Comparatively close positions of charales and land plants, chytrids and Zygomycetes, Physarum and amoeba, and red algae and green algae are also seen in this network.

Chromosome banding and compaction

We have described a characteristic substructure of mitotic chromosomes, the chromosomal unit fibre, with lengths about five times the length of the corresponding metaphase chromosomes and a uniform diameter of 0.4 micrometer. In order to study the relationship of chromosome banding to chromosome compaction, methods have been devised to obtain banding patterns on chromosomal unit fibres, similar to G-band patterns of intact mitotic chromosomes. The total number of bands plus interbands per haploid human karyotype is estimated at about 3000. The banding pattern of chromosomal unit fibres indicates a certain resemblance to the normal G-banding pattern of human chromosomes even if the details indicate a short-range random distribution.

The length of silver-stained human autosomal pachytene chromosomes

The length of 44 silver-stained human autosomal pachytene complements was shown to vary from about 300 micrometer to at least 535 micrometer. The lengths of the individual 22 autosomal chromosomes of eight complements representing this interval was measured and the relative lengths calculated. For most of the chromosomes a 1:1 relationship was found between the relative length and the corresponding relative DNA content (Mendelsohn et al. 1973). For some of the chromosomes this ratio seemed to deviate systematically from the 1:1 ratio. The data indicate a different organization of certain stages of the meiotic and the mitotic chromosome (Bak et al. 1979).

Protein-depleted chromosomes. I. Structure of isolated protein-depleted chromosomes

Protein-depleted isolated Chinese hamster chromosomes have been obtained by different protein extraction procedures and examined by electron microscopy and SDS-polyacrylamide gel electrophoresis. Salt-resistant centromeric and telomeric structures are visible in protein-depleted chromosomes and the protein-depleted chromosomes appear to have a regular, longitudinal pattern in critical point dried preparations. The scaffold-like structure of protein-depleted chromosomes is highly affected by the ionic strength and composition of the extraction medium and by the spreading conditions. Nucleosomal histones of isolated chromosomes proved to be more sensitive to the sodium chloride treatment than histones of isolated chromatin. A small, but constant quantity of core histones was detected in 2 M salt extracted chromosomes and H3 and H4 histones of isolated chromosomes appeared to be resistant to the sodium deoxycholate treatment.

On dinoflagellate evolution

A broad overview of the diversity of living dinoflagellates is presented in a hypothetical evolutionary context. Ultrastructural, and some physiological information is included. Five principal organizational types: prorocentroid, dinophysoid, gonyaulacoid, peridinioid and gymnodinoid, are taken to represent lineages, and the developments within each summarized. Thecal evolution is discussed party with the aid of a model developed to determine probable plate homologies in the gonyaulacoids and peridinioids. Both primitive and highly specialized features are drawn attention to, particularly with regard to the nucleus and ocelli. The parallelism between the latter and metazoan eyes is extraordinary, considering that the dinoflagellate organelles are made of subcellular components. The roles of various types of cysts within the lifecycle of dinoflagellates are discussed. The compatibility of the hypothetical events proposed here with the fossil record is briefly considered, and some indications of the phyletic position of dinoflagellates are reviewed. The conclusions summarize the principal developments that appear to have arisen within the group. The relative primitiveness of the desmokonts is affirmed. A new combination, Plectodinium miniatum (Kofoid and Swezy) comb. nov. is proposed, as well as the recognition of a new order, the Gonyaulacales ord. nov.