The problem of transition from the chemical to the biological evolution: Some possible solutions

On the basis of evidence that several low-molecular-weight substances as well as enzymes are compartmentalised within the socalled soluble phase of the cell, and other considerations, it is argued that DNA may not contain information for certain types of organisation found in living cells. It may be necessary for a cell to possess the non-DNA-controlled organisation for performance of its minimum functions; such organisation would then also serve as a template for its appearance in the daughter cell. The problem of transition from chemical to biological evolution (that is, the formation of the first cell) may be essentially the problem of emergence of such intracellular organisation for which information may not reside in DNA. Two possible mechanisms through which this may have happened are stated.     

Signalling: basics and evolution

Signalling concerns the transfer of information from one body, a source, to another, a receiver in order to stimulate activity. The problem arises with the word information. It is defined as what is transferred in a sequence of things, say between people, e.g. words or signs. The idea of signalling between people is then obvious but it is not clear in cell biology. Information transfer, signalling, is required for the organisation of all cellular activity but we must ask what is transferred and how is it transmitted and received? Sometimes it is assumed that all information, i.e. organisation in a cell, is represented in the DNA sequence. This is incorrect. We shall show that the environment is a second source of information concerning material and energy. The receiving party from both DNA and the environment is general metabolism. The metabolism then signals back and sends information to both DNA and uptake from the environment. Even then energy is needed with machinery to send out all signals. This paper examines the way signalling evolved from prokaryotes through to man. In this process the environmental information received increased to the extent that finally the brain is a phenotypic as much as a genotypic organ within a whole organism. By phenotypic we mean it is organised by and interactive with information from the environment.     

Constraints upon the organisation and evolution of chromosomes in Allium

Summary In terms of chromosome morphology, karyotype organisation, taxonomy and genetic relationship as judged from chromosome pairing in the Fl hybrid, A. cepa and A.fistulosum are two closely related species. But large variation in nuclear DNA amounts has occurred during the evolution of the two species. A comparison of the molecular composition of DNA in the two species has confirmed that the excess DNA acquired during evolution was predominantly repetitive sequences (sequences which do not encode genetic information). However, its distribution within the chromosome complements was equal in all chromosomes irrespective of the differences in chromosome size. The even distribution of the excess DNA within complements suggests strong constraints underlying evolutionary changes in genome organisation. The nature of the constraints is discussed, and it is shown that such constraints can influence the direction of karyotype evolution during speciation.     

Phylogenetic fate mapping: theoretical and experimental studies applied to the development of mouse fibroblasts

Mutations are an inevitable consequence of cell division. Similarly to how DNA sequence differences allow inferring evolutionary relationships between organisms, we and others have recently demonstrated how somatic mutations may be exploited for phylogenetically reconstructing lineages of individual cells during development in multicellular organisms. However, a problem with such "phylogenetic fate maps" is that they cannot be verified experimentally; distinguishing actual lineages within clonal populations requires direct observation of cell growth, as was used to construct the fate map of Caenorhabditis elegans, but is not possible in higher organisms. Here we employ computer simulation of mitotic cell division to determine how factors such as the quantity of cells, mutation rate, and the number of examined marker sequences contribute to fidelity of phylogenetic fate maps and to explore statistical methods for assessing accuracy. To experimentally evaluate these factors, as well as for the purpose of investigating the developmental origins of connective tissue, we have produced a lineage map of fibroblasts harvested from various organs of an adult mouse. Statistical analysis demonstrates that the inferred relationships between cells in the phylogenetic fate map reflect biological information regarding the origin of fibroblasts and is suggestive of cell migration during mesenchymal development.     

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.     

Modulation of apoptosis by starvation: morphological and biochemical study of rat intestinal mucosa

Morphology at light and electron microscopic levels, expression and activation of transglutaminase and DNA fragmentation at internucleosomal sites were used as markers to study the effect of starvation on the apoptosis of small intestinal epithelial cells. The cells entering apoptotic programme in well-fed animals undergo many morphological changes in apical cytoplasm involving alterations in actin cytoskeleton organisation which may cause a discharge of microvilli. Some free floating cells in the intestinal lumen show characteristics of apoptotic cell death, e.g. shrinkage of cell and peripheral condensation of chromatin, while mitochondria and lysosomes remain unchanged. Apoptotic bodies are also seen in scanning electron micrographs. During progressive starvation, epithelial cells do not enter the apoptotic cell death programme. Biochemical markers for apoptosis such as increased transglutaminase activity and DNA fragmentation are clearly discernible in normally fed animals. The percentage of cells labelled immunohistochemically by antibody against transglutaminase decreased during starvation while DNA fragmentation was absent. The exact mechanism for suppressing apoptosis in intestinal cells under starvation is not known. However, the data presented here support the existence of such a regulatory process.     

Genomic variability within an organism exposes its cell lineage tree

What is the lineage relation among the cells of an organism? The answer is sought by developmental biology, immunology, stem cell research, brain research, and cancer research, yet complete cell lineage trees have been reconstructed only for simple organisms such as Caenorhabditis elegans. We discovered that somatic mutations accumulated during normal development of a higher organism implicitly encode its entire cell lineage tree with very high precision. Our mathematical analysis of known mutation rates in microsatellites (MSs) shows that the entire cell lineage tree of a human embryo, or a mouse, in which no cell is a descendent of more than 40 divisions, can be reconstructed from information on somatic MS mutations alone with no errors, with probability greater than 99.95%. Analyzing all approximately 1.5 million MSs of each cell of an organism may not be practical at present, but we also show that in a genetically unstable organism, analyzing only a few hundred MSs may suffice to reconstruct portions of its cell lineage tree. We demonstrate the utility of the approach by reconstructing cell lineage trees from DNA samples of a human cell line displaying MS instability. Our discovery and its associated procedure, which we have automated, may point the way to a future "Human Cell Lineage Project" that would aim to resolve fundamental open questions in biology and medicine by reconstructing ever larger portions of the human cell lineage tree.     

The dragon on the gold: myths and realities for data mining in biomedicine and biotechnology using digital and molecular libraries

To develop bioscience and personalized medicine in the post-genomic era, the biggest problem may be how to extract knowledge from the rich libraries of biomedical data. A particular dragon protects the gold therein: the dragon is the "curse of dimensionality" and its formidable fire weapon, which is burning researchers, is the "combinatorial explosion". This arises because many genomic, proteomic, clinical, and lifestyle factors may interact that cannot necessarily be considered on a simple pairwise or additive basis. A suggested theoretical solution--or at least "road map" that ameliorates management of these problems--borrows from several disciplines. It is undertaken also in the hope might also lead to research with broader impact on several unresolved issues in biotechnology: conversely, mathematical understanding of processes involving molecular libraries, such as cDNA libraries and DNA in the living cell itself, may open the opportunities to use biotechnology to construct nanotechnological storage and query systems.     

Organization of brain complexity--synapse proteome form and function.

Proteomic study of the synapse has generated an extensive list of molecular components, revealing one of the most complex functional systems currently known to cell biology. While fundamental to neural information processing, behaviour and disease, the molecular organisation of the synapse and its relation to higher-level function has yet to be clearly understood. Neurotransmitter receptor complexes, such as the N-methyl-D-aspartate receptor complex (NRC/MASC), are major components of the synaptic proteome. We have recently completed a detailed study of MASC, its functional organisation and involvement in behaviour and disease. This pointed to simple design principles underlying synaptic organisation. Drawing together the results of proteomic and analytical study, we sketch out a model for synaptic functional organisation.     

Why do Neurons Enter the Cell Cycle?

Increasing evidence indicates that postmitotic, terminally differentiated neurons activate the cell cycle before death. The purpose of this cell cycle activation, however, remains elusive. In proliferating cells, cell cycle machinery is a major contributor to the DNA damage response, which is comprised of growth arrest. In quiescent cells such as terminally differentiated neurons, cell cycle-associated events may also be part of the DNA damage response. A link between DNA damage and repair, cell cycle regulation and cell death is becoming increasingly recognized for cycling cells but remains elusive for quiescent cells. Neurons are particularly susceptible to oxidative stress due to the high rate of oxidative metabolism in the brain and the low level of antioxidant enzymes compared to other somatic tissues. This is supported by fact that the intracellular end point of many neurotoxic stimuli is oxidative stress, which also represents a major cause of the neuropathology underlying a variety of neurodegenerative diseases. DNA is perhaps the major target of oxyradicals. Thus, oxidative stress may cause DNA damage, which is countered by a complex defense mechanism, the DNA damage response, which involves not only the elimination of DNA damage, but its coordination with other cellular processes such as cell-cycle progression, together directing to preserve genomic integrity. The function of such response is the removal of DNA damage by DNA repair pathways, or the elimination of damaged cells via apoptosis. The present review discusses the idea that the cell cycle machinery is a critical element of the DNA damage response not only in cycling, but also quiescent cells, and may bear the same function: to repair the damage or initiate apoptosis if the damage is too extensive to be repaired.     

An information-theory model of cellular survival, mutation and transformation and the relevance of this model to chemical carcinogenesis

A model of cellular survival, mutation and transformation is presented in accordance with information theory. A cellular system is considered to be stable with respect to its environment when the vital information the cell expresses at least equals the information requirements of the environment. Environmental agents, such as mutagens, perturb the cell's expression of information such that an imbalance occurs between the cell's information requirement and the cell's ability to express vital information. This imbalance, which is interpreted as the intrinsic entropy of the cell, serves as a measure of biological cell death. If the cell compensates for the altered ability to express information by adapting to a less restricted set of information requirements, then one may view the cell as having undergone a "transformation" to a less restricted phenotype. This paper will elucidate the mathematical inter-relationships of cellular survival, mutation and transformation and will relate these mathematical concepts to chemical carcinogenesis.     

Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell

The organisation of cells of the planctomycete species Pirellula marina, Isosphaera pallida, Gemmata obscuriglobus, Planctomyces maris and "Candidatus Brocadia anammoxidans" was investigated based on ultrastructure derived from thin-sections of cryosubstituted cells, freeze-fracture replicas, and in the case of Gemmata obscuriglobus and Pirellula marina, computer-aided 3-D reconstructions from serial sections of cryosubstituted cells. All planctomycete cells display a peripheral ribosome-free region, termed here the paryphoplasm, surrounding the perimeter of the cell, and an interior region including any nucleoid regions as well as ribosome-like particles, bounded by a single intracytoplasmic membrane (ICM), and termed the pirellulosome in Pirellula species. Immunogold labelling and RNase-gold cytochemistry indicates that in planctomycetes all the cell DNA is contained wholly within the interior region bounded by the ICM, and the paryphoplasm contains no DNA but at least some of the cell's RNA. The ICM in Isosphaera pallida and Planctomyces maris is invaginated such that the paryphoplasm forms a major portion of the cell interior in sections, but in other planctomycetes it remains as a peripheral zone. In the anaerobic ammonium-oxidising ("anammox" process) chemoautotroph "Candidatus Brocadia anammoxidans" the interior region bounded by ICM contains a further internal single-membrane-bounded region, the anammoxosome. In Gemmata obscuriglobus, the interior ICM-bounded region contains the nuclear body, a double-membrane-bounded region containing the cell's nucleoid and all genomic DNA in addition to some RNA. Shared features of cell compartmentalisation in different planctomycetes are consistent with the monophyletic nature of the planctomycetes as a distinct division of the Bacteria. The shared organisational plan for the planctomycete cell constitutes a new type not known in cells of other bacteria.     

Biolistic plant transformation

The biolistic process represents a completely new approach to the problem of how to deliver DNA into intact cells and tissues. High velocity microprojectiles are used to carry DNA or other substances past cell walls and membranes. Because DNA is being 'shot' into cells, it represents a type of biological ballistics, hence the term "biolistics".
There are several fundamental advantages to the biolistic process over other plant transformation techniques. The biolistic process appears to be effective regardless of species or tissue type, it is a rapid and very simple procedure, and it should facilitate the direct transformation of totipotent tissues such as pollen, embryos, meristems and morphogenic cell cultures. In addition, the biolistic process appears to be uniquely suitable for organelle transformation.
The disadvantages of the biolistic process are that it requires special instrumentation, and is still in the early stages of its development. Consequently, delivery efficiencies are still not as high as can be achieved in highly optimized transformation systems such as electroporation or agrobacterial-infection of tobacco. Furthermore, potential users should be prepared to spend some time adapting existing protocols to their specific species or tissue of interest.     

Polite DNA: Functional density and functional compatibility in genomes

Summary Certain as yet poorly defined functions of DNA appear to involve collectively domain-sized sequences. It is proposed that most sequence segments within a domain may be either functionally superfluous or instrumental, depending on how many related sequences are present in the domain. When redundant and functionally dispensable, such DNA segments presumably still have to conform to compositional or sequence-motif patterns that characterize the domain. In its relations with neighboring sequences, such DNA is required to be polite. Polite DNA is DNA that, without being crucially involved in function, is subject to constraints of conformity and, through its base composition, respects a function for which it is not required. This concept is developed by contrasting the distribution of specific and general functions over DNA with this distribution as found in proteins and by distinguishing functional compatibility from pivotal functionality. The sequence constraints to which heterochromatin as well as, apparently, long interspersed repetitive sequences are known to be subject seem to imply that DNA, even when it does not carry out a pivotal function, is indeed, at the very least, required to be polite.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

New findings showing how DNA methylation influences diseases

In 1975, Holliday and Pugh as well as Riggs independently hypothesized that DNA methylation in eukaryotes could act as a hereditary regulation mechanism that influences gene expression and cell differentiation. Interest in the study of epigenetic processes has been inspired by their reversibility as well as their potentially preventable or treatable consequences. Recently, we have begun to understand that the features of DNA methylation are not the same for all cells.Major differences have been found between differentiated cells and stem cells.Methylation influences various pathologies, and it is very important to improve the understanding of the pathogenic mechanisms. Epigenetic modifications may take place throughout life and have been related to cancer, brain aging, memory disturbances, changes in synaptic plasticity, and neurodegenerative diseases,such as Parkinson's disease and Huntington's disease. DNA methylation also has a very important role in tumor biology. Many oncogenes are activated by mutations in carcinogenesis. However, many genes with tumor-suppressor functions are "silenced" by the methylation of CpG sites in some of their regions.Moreover, the role of epigenetic alterations has been demonstrated in neurological diseases. In neuronal precursors, many genes associated with development and differentiation are silenced by CpG methylation. In addition,recent studies show that DNA methylation can also influence diseases that do not appear to be related to the environment, such as IgA nephropathy, thus affecting,the expression of some genes involved in the T-cell receptor signaling. In conclusion, DNA methylation provides a whole series of fundamental information for the cell to regulate gene expression, including how and when the genes are read, and it does not depend on the DNA sequence.     

Life, self-reproduction and information: beyond the machine metaphor

The problem of representing information in automation models of self-replication is considered. It is shown that, unlike in the natural reproduction process, in a computable model the reproduced entities do not contain all the information necessary for guiding the process. Current theoretical understanding of life and its replication, based on such models, is argued to be essentially inadequate. The solution to this problem is claimed to require recognition of the theoretical fact that information in living systems is different from that subsumed under the category of "knowledge", which is representable as computer programs or triggers of state transitions. A discussion of fundamentals of a new theory of information and its relationship to replication models is given and a new direction of further developments of biological theories is envisioned.     

A Bayesian Approach to Assessing the Superiority of a Dose Combination

One prevalent goal within clinical trials is to determine whether or not a combination of two drugs is more effective than each of its components. Many researchers have addressed this issue for fixed-dose combination trials, using frequentist hypothesis testing techniques. In addition, several of these have incorporated prior information from sources such as Phase II trials or expert opinions. The Bayesian approach to the general selection problem naturally accomodates the need to utilize such information. It is useful in the dose combination problem because it does not rely on a nuisance parameter that affects the power of frequentist procedures. We show that hierarchical Bayesian methods may be easily applied to this problem, yielding the probability that a drug combination is superior to its components. Moreover, we present methods that may be implemented using readily available software for numerical integration as well as ones that incorporate Markov Chain Monte Carlo methods.     

Growth-phase-dependent response to DNA damage in poly(ADP-ribose) polymerase deficient cell lines: basis for a new hypothesis describing the role of poly(ADP-ribose) polymerase in DNA replication and repair

We have studied the role of poly(ADP-ribose) polymerase in the repair of DNA damage induced by x-ray and N-methyl N-nitro-N-nitrosoguanidine (MNNG) by using V79 chinese hamster cells, and two derivative mutant cell lines, ADPRT54 and ADPRT351, that are deficient in poly(ADP-ribose) polymerase activity. Under exponentially growing conditions these mutant cell lines are hypersensitive to x-irradiation and MNNG compared to their parental V79 cells which could be interpreted to suggest that poly(ADP-ribose) polymerase is involved in the repair of DNA damage. However, the level of DNA strand breaks induced by x-irradiation and MNNG and their rates of repair are similar in all the cell lines, thus suggesting that it may not be the difference in strand break formation or in its rate of repair that is contributing to the enhanced cell killing in exponentially growing poly(ADP-ribose) polymerase deficient cell lines. In contrast, under growth-arrested conditions, all three cell lines become similarly sensitive to both x-irradiation and MNNG, thus suggesting that poly(ADP-ribose) polymerase may not be involved in the repair of DNA damage in growth-arrested cells. These paradoxical results could be interpreted to suggest that poly(ADP-ribose) polymerase is involved in DNA repair in a cell-cycle-dependent fashion, however, it is functionally active throughout the cell cycle. To resolve this dilemma and explain these results and those obtained by many others, we propose that the normal function of poly(ADP-ribose) polymerase is to prevent DNA recombination processes and facilitate DNA ligation.