Roles Of Deoxyribonucleic Acid in Inheritance

Is RNA the working genome in eukaryotes ? The 60 year evolution of a conceptual challenge

About 80 years ago, in 1943, after a century of biochemical and genetic research, DNA was established as the carrier of genetic information. At the onset of Molecular Biology around 1960, the genome of living organisms embodied 3 basic, still unknown paradigms: its composition, organisation and expression. Between 1980 and 1990, its replication was understood, and ideas about its 3D-organisation were suggested and finally confirmed by 2010. The basic mechanisms of gene expression in higher organisms, the synthesis of precursor RNAs and their processing into functional RNAs, were also discovered about 60 years ago in 1961/62. However, some aspects were then, and are still now debated, although the latest results in post-genomic research have confirmed the basic principles. When my history-essay was published in 2003, describing the discovery of RNA processing 40 years earlier, the main facts were not yet generally confirmed or acknowledged. The processing of pre-rRNA to 28 S and 18 S rRNA was clearly demonstrated, confirmed by others and generally accepted as a fact. However, the "giant" size of pre-mRNA 10-100 kb-long and pervasive DNA transcription were still to be confirmed by post-genomic methods. It was found, surprisingly, that up to 90% of DNA is transcribed in the life cycle of eukaryotic organisms thus showing that pervasive transcription was the general rule. In this essay, we shall take a journey through the 60-year history of evolving paradigms of gene expression which followed the emergence of Molecular Biology, and we will also evoke some of the "folklore" in research throughout this period. Most important was the growing recognition that although the genome is encoded in DNA, the Working Genome in eukaryotic organisms is RNA.

The limiting effect of genome size on xylem vessel diameter is shifted by environmental pressures in seed plants

Current and previous studies have extensively studied the physiological and ecological consequences of genome size (GS) on plants because of the limiting effect of GS on cell size. However, it is still obscure whether such limiting effect could be shifted by environmental pressures, or not. Here, we compiled a global dataset comprised of GS, xylem vessel diameter (V _dia), xylem hydraulic conductivity (K _S), P ₅₀ (xylem water potential at the loss of 50% maximum K _S), and climate factors of 251 phylogeny and habitat divergent species from 59 families. The results showed that GS could limit the V _dia of the species from the same family sampled in the similar climate conditions. But the expected positive relationship between GS and V _dia became uncertain and even negative across different environmental conditions. V _dia was strongly positively coordinated with mean annual temperature (MAT), mean annual precipitation (MAP), and potential evapotranspiration (PET). Furthermore, V _dia as the anatomic foundation of plant hydraulic performance was strongly positively coordinated with K _S and negatively coordinated with -P ₅₀. The strong environmental selection on K _S and P ₅₀ explained the concerted regulation of V _dia by environmental factors. The findings revealed the combined regulation of GS and environmental pressures on xylem cell size and thus affected plant eco-physiological performance. The shifted cell size limiting effect of GS by environmental factors manifests plants great plasticity under changed environmental conditions.

Myonuclear content regulates cell size with similar scaling properties in mice and humans

Muscle fibers are the largest cells in the body, and one of its few syncytia. Individual cell sizes are variable and adaptable, but what governs cell size has been unclear. We find that muscle fibers are DNA scarce compared to other cells, and that the nuclear number (N) adheres to the relationship N = aVb where V is the cytoplasmic volume. N invariably scales sublinearly to V (b < 1), making larger cells even more DNA scarce. N scales linearly to cell surface in adult humans, in adult and developing mice, and in mice with genetically reduced N, but in the latter the relationship eventually fails when they reach adulthood with extremely large myonuclear domains. Another exception is denervation-atrophy where nuclei are not eliminated. In conclusion, scaling exponents are remarkably similar across species, developmental stages and experimental conditions, suggesting an underlying scaling law where DNA-content functions as a limiter of muscle cell size.

Replicating and Cycling Stores of Information Perpetuate Life

Life is perpetuated through a single-cell bottleneck between generations in many organisms. Here, I highlight that this cell holds information in two distinct stores: in the linear DNA sequence that is replicated during cell divisions, and in the three-dimensional arrangement of molecules that can change during development but is recreated at the start of each generation. These two interdependent stores of information - one replicating with each cell division and the other cycling with a period of one generation - coevolve while perpetuating an organism. Unlike the genome sequence, the arrangement of molecules, including DNA, RNAs, proteins, sugars, lipids, etc., is not well understood. Because this arrangement and the genome sequence are transmitted together from one generation to the next, analysis of both is necessary to understand evolution and origins of inherited diseases. Recent developments suggest that tools are in place to examine how all the information to build an organism is encoded within a single cell, and how this cell code is reproduced in every generation. See also the video abstract here: https://youtu.be/IdWEL-T6TPU.

Nuclear DNA content correlates with depth, body size, and diversification rate in amphipod crustaceans from ancient Lake Baikal, Russia

Lake Baikal in Russia is a large, ancient lake that has been the site of a major radiation of amphipod crustaceans. Nearly 400 named species are known in this single lake, and it is thought that many more await description. The size and depth of Lake Baikal, in particular, may have contributed to the radiation of endemic amphipods by providing a large number of microhabitats for species to invade and subsequently experience reproductive isolation. Here we investigate the possibility that large-scale genomic changes have also accompanied diversification in these crustaceans. Specifically, we report genome size estimates for 36 species of Baikal amphipods, and examine the relationship between genome size, body size, and the maximum depths at which the amphipods are found in the lake. Genome sizes ranged nearly 8-fold in this sample of amphipod species, from 2.15 to 16.63 pg, and there were significant, positive, phylogenetically corrected relationships between genome size, body size, maximum depth, and diversification rate among these species. Our results suggest that major genomic changes, including transposable element proliferation, have accompanied speciation that was driven by selection for differences in body size and habitat preference in Lake Baikal amphipods.

The protist Trichomonas vaginalis harbors multiple lineages of transcriptionally active Mutator-like elements

Background

For three decades the Mutator system was thought to be exclusive of plants, until the first homolog representatives were characterized in fungi and in early-diverging amoebas earlier in this decade.

Results

Here, we describe and characterize four families of Mutator-like elements in a new eukaryotic group, the Parabasalids. These Trichomonas vaginalis Mutator- like elements, or TvMULEs, are active in T. vaginalis and patchily distributed among 12 trichomonad species and isolates. Despite their relatively distinctive amino acid composition, the inclusion of the repeats TvMULE1, TvMULE2, TvMULE3 and TvMULE4 into the Mutator superfamily is justified by sequence, structural and phylogenetic analyses. In addition, we identified three new TvMULE-related sequences in the genome sequence of Candida albicans. While TvMULE1 is a member of the MuDR clade, predominantly from plants, the other three TvMULEs, together with the C. albicans elements, represent a new and quite distinct Mutator lineage, which we named TvCaMULEs. The finding of TvMULE1 sequence inserted into other putative repeat suggests the occurrence a novel TE family not yet described.

Conclusion

These findings expand the taxonomic distribution and the range of functional motif of MULEs among eukaryotes. The characterization of the dynamics of TvMULEs and other transposons in this organism is of particular interest because it is atypical for an asexual species to have such an extreme level of TE activity; this genetic landscape makes an interesting case study for causes and consequences of such activity. Finally, the extreme repetitiveness of the T. vaginalis genome and the remarkable degree of sequence identity within its repeat families highlights this species as an ideal system to characterize new transposable elements.

The problem of the eukaryotic genome size

The current state of knowledge concerning the unsolved problem of the huge interspecific eukaryotic genome size variations not correlating with the species phenotypic complexity (C-value enigma also known as C-value paradox) is reviewed. Characteristic features of eukaryotic genome structure and molecular mechanisms that are the basis of genome size changes are examined in connection with the C-value enigma. It is emphasized that endogenous mutagens, including reactive oxygen species, create a constant nuclear environment where any genome evolves. An original quantitative model and general conception are proposed to explain the C-value enigma. In accordance with the theory, the noncoding sequences of the eukaryotic genome provide genes with global and differential protection against chemical mutagens and (in addition to the anti-mutagenesis and DNA repair systems) form a new, third system that protects eukaryotic genetic information. The joint action of these systems controls the spontaneous mutation rate in coding sequences of the eukaryotic genome. It is hypothesized that the genome size is inversely proportional to functional efficiency of the anti-mutagenesis and/or DNA repair systems in a particular biological species. In this connection, a model of eukaryotic genome evolution is proposed.

Genome size is a strong predictor of cell size and stomatal density in angiosperms

Across eukaryotes phenotypic correlations with genome size are thought to scale from genome size effects on cell size. However, for plants the genome/cell size link has only been thoroughly documented within ploidy series and small subsets of herbaceous species. Here, the first large-scale comparative analysis is made of the relationship between genome size and cell size across 101 species of angiosperms of varying growth forms. Guard cell length and epidermal cell area were used as two metrics of cell size and, in addition, stomatal density was measured. There was a significant positive relationship between genome size and both guard cell length and epidermal cell area and a negative relationship with stomatal density. Independent contrast analyses revealed that these traits are undergoing correlated evolution with genome size. However, the relationship was growth form dependent (nonsignificant results within trees/shrubs), although trees had the smallest genome/cell sizes and the highest stomatal density. These results confirm the generality of the genome size/cell size relationship. The results also suggest that changes in genome size, with concomitant influences on stomatal size and density, may influence physiology, and perhaps play an important genetic role in determining the ecological and life-history strategy of a species.

Gene and genon concept: coding versus regulation. A conceptual and information-theoretic analysis of genetic storage and expression in the light of modern molecular biology

We analyse here the definition of the gene in order to distinguish, on the basis of modern insight in molecular biology, what the gene is coding for, namely a specific polypeptide, and how its expression is realized and controlled. Before the coding role of the DNA was discovered, a gene was identified with a specific phenotypic trait, from Mendel through Morgan up to Benzer. Subsequently, however, molecular biologists ventured to define a gene at the level of the DNA sequence in terms of coding. As is becoming ever more evident, the relations between information stored at DNA level and functional products are very intricate, and the regulatory aspects are as important and essential as the information coding for products. This approach led, thus, to a conceptual hybrid that confused coding, regulation and functional aspects. In this essay, we develop a definition of the gene that once again starts from the functional aspect. A cellular function can be represented by a polypeptide or an RNA. In the case of the polypeptide, its biochemical identity is determined by the mRNA prior to translation, and that is where we locate the gene. The steps from specific, but possibly separated sequence fragments at DNA level to that final mRNA then can be analysed in terms of regulation. For that purpose, we coin the new term "genon". In that manner, we can clearly separate product and regulative information while keeping the fundamental relation between coding and function without the need to introduce a conceptual hybrid. In mRNA, the program regulating the expression of a gene is superimposed onto and added to the coding sequence in cis - we call it the genon. The complementary external control of a given mRNA by trans-acting factors is incorporated in its transgenon. A consequence of this definition is that, in eukaryotes, the gene is, in most cases, not yet present at DNA level. Rather, it is assembled by RNA processing, including differential splicing, from various pieces, as steered by the genon. It emerges finally as an uninterrupted nucleic acid sequence at mRNA level just prior to translation, in faithful correspondence with the amino acid sequence to be produced as a polypeptide. After translation, the genon has fulfilled its role and expires. The distinction between the protein coding information as materialised in the final polypeptide and the processing information represented by the genon allows us to set up a new information theoretic scheme. The standard sequence information determined by the genetic code expresses the relation between coding sequence and product. Backward analysis asks from which coding region in the DNA a given polypeptide originates. The (more interesting) forward analysis asks in how many polypeptides of how many different types a given DNA segment is expressed. This concerns the control of the expression process for which we have introduced the genon concept. Thus, the information theoretic analysis can capture the complementary aspects of coding and regulation, of gene and genon.

IsPalaeospondylus gunni a fossil larval lungfish? Insights fromNeoceratodus forsteri development

The enigmatic Devonian fossil Palaeospondylus gunni was identified as a larval form, metamorphosing into the lungfish Dipterus valenciennesi. Morphological features used to identify P. gunni as a larval lungfish include enlarged cranial ribs, rudimentary limb girdles, and absence of teeth. However, this combination of features does not characterize the extant lungfish Neoceratodus forsteri, even at very young stages, nor early stages of Devonian and younger fossil lungfish. Absence of teeth is problematic because early ontogenetic stages of fossil and living lungfish possess full dentitions including marginal teeth. Also problematic are cranial ribs as a defining character of lungfish, as these also occur in certain actinopterygians. It is argued that Neoceratodus is an obligate neotene (reproductively mature larva), with the implication that metamorphosis was a feature of the ontogeny of early lungfish. Pedomorphic characters have been recognized in Neoceratodus and other post-Devonian lungfish, including large cells and correspondingly large genome size; these latter characters correlate with neoteny in salamanders. Small cells preserved in fossil bone suggest that Devonian lungfish had a smaller genome than post-Devonian lungfish, implying that they were not neotenic. As fossil lungfish cell sizes (and genomes) increased in the late Paleozoic, the diversity of lungfish morphologies decreased, so that taxa like Sagenodus and Conchopoma show morphological similarity to Neoceratodus, marking a point in phylogeny at which metamorphosis was potentially lost. Since ancestral larval characters are retained in neotenic adults, we predict that Devonian larvae should resemble these post-Devonian taxa, a prediction which Palaeospondylus does not fulfill.

Streamlining and simplification of microbial genome architecture

The genomes of unicellular species, particularly prokaryotes, are greatly reduced in size and simplified in terms of gene structure relative to those of multicellular eukaryotes. Arguments proposed to explain this disparity include selection for metabolic efficiency and elevated rates of deletion in microbes, but the evidence in support of these hypotheses is at best equivocal. An alternative explanation based on fundamental population-genetic principles is proposed here. By increasing the mutational target sizes of associated genes, most forms of nonfunctional DNA are opposed by weak selection. Free-living microbial species have elevated effective population sizes, and the consequent reduction in the power of random genetic drift appears to be sufficient to enable natural selection to inhibit the accumulation of excess DNA. This hypothesis provides a potentially unifying explanation for the continuity in genomic scaling from prokaryotes to multicellular eukaryotes, the divergent patterns of mitochondrial evolution in animals and land plants, and various aspects of genomic modification in microbial endosymbionts.

[Noncoding sequences of the eukaryotic genome as an additional protection of genes from chemical mutagens]

A quantitative model was developed that detects a new function of noncoding sequences in the eukaryotic genome, namely, the protection of coding sequences from chemical (mainly endogenous) mutagens. It was shown that, under common ecological conditions, the number of nucleotides damaged by mutagens in coding sequences of the genome is inversely proportional to the size of their noncoding counterparts. Noncoding sequences can differently protect single genetic loci from chemical mutagens by the formation of specific spatial structures of the protected loci in the interphase nuclei. The significant differences in genome sizes between species (paradox C) can be explained by different contributions of noncoding sequences to the total effect of genome protection from endogenous chemical mutagens.

Cell size as a link between noncoding DNA and metabolic rate scaling

Accumulation of noncoding DNA and therefore genome size (C-value) may be under strong selection toward increase of body size accompanied by low metabolic costs. C-value directly affects cell size and specific metabolic rate indirectly. Body size can enlarge through increase of cell size and/or cell number, with small cells having higher metabolic rates. We argue that scaling exponents of interspecific allometries of metabolic rates are by-products of evolutionary diversification of C-values within narrow taxonomic groups, which underlines the participation of cell size and cell number in body size optimization. This optimization leads to an inverse relation between slopes of interspecific allometries of metabolic rates and C-value. To test this prediction we extracted literature data on basal metabolic rate (BMR), body mass, and C-value of mammals and birds representing six and eight orders, respectively. Analysis of covariance revealed significant heterogeneity of the allometric slopes of BMR and C-value in both mammals and birds. As we predicted, the correlation between allometric exponents of BMR and C-value was negative and statistically significant among mammalian and avian orders.

The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes

Cytological and organismal characteristics associated with cellular DNA content underpin most adaptionist interpretations of genome size variation. Since fishes are the only group of vertebrate for which relationships between genome size and key cellular parameters are uncertain, the cytological correlates of genome size were examined in this group. The cell and nuclear areas of erythrocytes showed a highly significant positive correlation with each other and with genome size across 22 cartilaginous and 201 ray-finned fishes. Regressions remained significant at all taxonomic levels, as well as among different fish lineages. However, the results revealed that cartilaginous fishes possess higher cytogenomic ratios than ray-finned fishes, as do cold-water fishes relative to their warm-water counterparts. Increases in genome size owing to ploidy shifts were found to influence cell and nucleus size in an immediate and causative manner, an effect that persists in ancient polyploid lineages. These correlations with cytological parameters known to have important influences on organismal phenotypes support an adaptive interpretation for genome size variation in fishes.

Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae)

Chloroplasts originated just once, from cyanobacteria enslaved by a biciliate protozoan to form the plant kingdom (green plants, red and glaucophyte algae), but subsequently, were laterally transferred to other lineages to form eukaryote-eukaryote chimaeras or meta-algae. This process of secondary symbiogenesis (permanent merger of two phylogenetically distinct eukaryote cells) has left remarkable traces of its evolutionary role in the more complex topology of the membranes surrounding all non-plant (meta-algal) chloroplasts. It took place twice, soon after green and red algae diverged over 550 Myr ago to form two independent major branches of the eukaryotic tree (chromalveolates and cabozoa), comprising both meta-algae and numerous secondarily non-photosynthetic lineages. In both cases, enslavement probably began by evolving a novel targeting of endomembrane vesicles to the perialgal vacuole to implant host porter proteins for extracting photosynthate. Chromalveolates arose by such enslavement of a unicellular red alga and evolution of chlorophyll c to form the kingdom Chromista and protozoan infrakingdom Alveolata, which diverged from the ancestral chromalveolate chimaera. Cabozoa arose when the common ancestor of euglenoids and cercozoan chlorarachnean algae enslaved a tetraphyte green alga with chlorophyll a and b. I suggest that in cabozoa the endomembrane vesicles originally budded from the Golgi, whereas in chromalveolates they budded from the endoplasmic reticulum (ER) independently of Golgi-targeted vesicles, presenting a potentially novel target for drugs against alveolate Sporozoa such as malaria parasites and Toxoplasma. These hypothetical ER-derived vesicles mediated fusion of the perialgal vacuole and rough ER (RER) in the ancestral chromist, placing the former red alga within the RER lumen. Subsequently, this chimaera diverged to form cryptomonads, which retained the red algal nucleus as a nucleomorph (NM) with approximately 464 protein-coding genes (30 encoding plastid proteins) and a red or blue phycobiliprotein antenna pigment, and the chromobiotes (heterokonts and haptophytes), which lost phycobilins and evolved the brown carotenoid fucoxanthin that colours brown seaweeds, diatoms and haptophytes. Chromobiotes transferred the 30 genes to the nucleus and lost the NM genome and nuclear-pore complexes, but retained its membrane as the periplastid reticulum (PPR), putatively the phospholipid factory of the periplastid space (former algal cytoplasm), as did the ancestral alveolate independently. The chlorarachnean NM has three minute chromosomes bearing approximately 300 genes riddled with pygmy introns. I propose that the periplastid membrane (PPM, the former algal plasma membrane) of chromalveolates, and possibly chlorarachneans, grows by fusion of vesicles emanating from the NM envelope or PPR. Dinoflagellates and euglenoids independently lost the PPM and PPR (after diverging from Sporozoa and chlorarachneans, respectively) and evolved triple chloroplast envelopes comprising the original plant double envelope and an extra outermost membrane, the EM, derived from the perialgal vacuole. In all metaalgae most chloroplast proteins are coded by nuclear genes and enter the chloroplast by using bipartite targeting sequences--an upstream signal sequence for entering the ER and a downstream chloroplast transit sequence. I present a new theory for the four-fold diversification of the chloroplast OM protein translocon following its insertion into the PPM to facilitate protein translocation across it (of both periplastid and plastid proteins). I discuss evidence from genome sequencing and other sources on the contrasting modes of protein targeting, cellular integration, and evolution of these two major lineages of eukaryote "cells within cells". They also provide powerful evidence for natural selection's effectiveness in eliminating most functionless DNA and therefore of a universally useful non-genic function for nuclear non-coding DNA, i.e. most DNA in the biosphere, and dramatic examples of genomic reduction. I briefly argue that chloroplast replacement in dinoflagellates, which happened at least twice, may have been evolutionarily easier than secondary symbiogenesis because parts of the chromalveolate protein-targeting machinery could have helped enslave the foreign plastids.

A bird's-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class aves

For half a century, variation in genome size (C-value) has been an unresolved puzzle in evolutionary biology. While the initial "C-value paradox" was solved with the discovery of noncoding DNA, a much more complex "C-value enigma" remains. The present study focuses on one aspect of this puzzle, namely the small genome sizes of birds. Significant negative correlations are reported between resting metabolic rate and both C-value and erythrocyte size. Cell size is positively correlated with both nucleus size and C-value in birds, as in other vertebrates. These findings shed light on the constraints acting on genome size in birds and illustrate the importance of interactions among various levels of the biological hierarchy, ranging from the subchromosomal to the ecological. Following from a discussion of the mechanistic bases of the correlations reported and the processes by which birds achieved and/or maintain small genomes, a pluralistic approach to the C-value enigma is recommended.

The bigger the C-value, the larger the cell: genome size and red blood cell size in vertebrates

Vertebrate genome sizes vary roughly 350-fold and correlate with a variety of cellular and organismal parameters. Most notable among these is the relationship between genome size ("C-value") and red blood cell (RBC) size, which can be identified within and among each of the five vertebrate classes. This relationship, in turn, leads to important associations between genome size and features such as metabolic rate (at least in homeotherms). The present article describes the correlation between genome size and RBC size in vertebrates and discusses some of the cytological, physiological, and evolutionary implications of this relationship.

Nucleotypic effects without nuclei: genome size and erythrocyte size in mammals

Previously reported haploid genome sizes (C-values) and erythrocyte sizes (measured as mean dry diameters) were compared for 67 species of mammals representing 31 families and 16 orders. Measurements on erythrocytes of four species of bats were also included in the study. Erythrocyte size was significantly positively correlated with genome size at each of the specific, generic, familial, and ordinal levels, with the relationship becoming much stronger following the exclusion of the order Artiodactyla, a group unique among mammals in terms of red blood cell morphology. Physiologically, these results are relevant in light of the known relationship between C-value and mass-corrected metabolic rate in homeotherms. In evolutionary terms, they provide insights into the constraints on genome expansion among mammals and are therefore of interest in attempts to solve the long-standing C-value enigma (also known as the C-value paradox).

Evolutionary implications of the relationship between genome size and body size in flatworms and copepods

Genome and body sizes were measured in 38 species of turbellarian flatworms and 16 species of copepod crustaceans. Significant positive relationships existed between genome size and body size in both groups. The slopes of these regressions indicated that increases in cell volume are reinforced by increased cell numbers, or that cell volumes show positive allometric variation with genome size. Genome sizes appear to vary in a discontinuous fashion among congeneric species in both groups, indicating that such changes have occurred rapidly, and with potentially profound effects on important morphological characters.

The duration of meiosis

A survey of work on meiotic duration in diploid plants shows that the duration is positively correlated with the DNA content per nucleus and with the mitotic cycle time. However, meiotic duration is not solely determined by the DNA content per nucleus but is also affected by chromosomal organization, DNA structure and the developmental pattern of the organism. Thus, in three polyploid plant species meiosis is much shorter and in three animal species it is much longer than would be expected in diploid plant species having corresponding DNA contents. Differences in meiotic duration in plant species are usually the result of proportional differences in all the stages of meiosis. Factors affecting the initiation, control and duration of meiosis are discussed. The consequences of changes in nuclear DNA content on developmental processes and the life cycle in plants are considered. It is suggested that DNA influences development in two ways, first directly through its informational content, and second indirectly by the physical mechanical effects of its mass independent of its informational content.

Genome size variation and its phenotypic consequences in Phyllotis rodents

Constitutive heterochromatin and genome size were studied in Phyllotis darwini, three Phyllotis xanthopygus subspecies, and their interspecific laboratory hybrids. P. darwini, with no or only small C-bands, had the smallest genome size; P. xanthopygus rupestris and P. x. vaccarum, with large C-bands in all the chromosomes, had the largest; and P. x. xanthopygus, with heterochromatin only in a few chromosomes, showed intermediate genome size. To examine some phenotypic consequences of nuclear DNA content, we measured nuclear and cellular surfaces and volumes. Linear regression analyses showed that all these cellular characters had a highly significant direct relationship with genome size. Hybrids had always the expected intermediate parental characteristics. Previous results indicate that P. x. vaccarum should have longer mitotic cycles and lower reproductive capacity than P. darwini. Our findings suggest that the "nucleotypic DNA" hypothesis, which considers genome size as an adaptive feature in higher plants and lower vertebrates, could be extended to these mammals. The analysis of heterochromatin and nuclear DNA amounts of other phyllotine and akodontine rodents supports the idea that small C-bands and genomes are ancestral conditions, from which independent and parallel events occurred until large genomes were produced.

A unified matrix hypothesis of DNA-directed morphogenesis, protodynamism and growth control

A theoretical concept is proposed, in order to explain some enigmatic aspects of cellular and molecular biology of eukaryotic organisms. Among these are the C-value paradox of DNA redundancy, the correlation of DNA content and cell size, the disruption of genes at DNA level, the "Chromosome field" data of Lima de Faria (Hereditas 93:1, 1980), the "quantal mitosis" proposition of Holtzer et al. (Curr. Top. Dev. Biol. 7:229 1972), the inheritance of morphological patterns, the relations of DNA and chromosome organisation to cellular structure and function, the molecular basis of speciation, etc. The basic proposition of the "Unified Matrix Hypothesis" is that the nuclear DNA has a direct morphogenic function, in addition to its coding function in protein synthesis. This additional genetic information is thought to be largely contained in the non-protein coding transcribed DNA, and in the untranscribed part of the genome.

The solution to the cytological paradox of isomorphy

Cells with polyploid nuclei are generally larger than cells of the same organism or species with nonpolyploid nuclei. However, no such change of cell size with ploidy level is observed in those red algae which alternate isomorphic haploid with diploid generations. The results of this investigation reveal the explanation. Nuclear DNA content and other parameters were measured in cells of the filamentous red alga Griffithsia pacifica. Nuclei of the diploid generation contain twice the DNA content of those of the haploid generation. However, all cells except newly formed reproductive cells are multinucleate. The nuclei are arranged in a nearly perfect hexagonal array just beneath the cell surface. When homologous cells of the two generations are compared, although the cell size is nearly identical, each nucleus of the diploid cell is surrounded by a region of cytoplasm (a "domain") nearly twice that surrounding a haploid nucleus. Cytoplasmic domains associated with a diploid nucleus contain twice the number of plastids, and consequently twice the amount of plastid DNA, than is associated with the domain of a haploid nucleus. Thus, doubling of ploidy is reflected in doubling of the size and organelle content of the domain associated with each nucleus. However, cell size does not differ between homologous cells of the two generations, because total nuclear DNA (sum of the DNA in all nuclei in a cell) per cell does not differ. This is the solution to the cytological paradox of isomorphy.

Hemostatic regulation and Whitehead's philosophy of organism

Biology as a scientific discipline has relied heavily upon advances in chemistry and physics. An inherent danger in this relationship is the reduction of living phenomena to physico-chemical terms. Whitehead's 'Philosophy of Organism' is utilized to examine current methodologies within biology and to evaluate their appropriateness for future research. Hemostatic regulation is employed to illustrate the applications of organistic concepts to biological research. It is concluded that understanding of living entities and their properties as well as possibly life itself will require synthesis of the many analytical elements as informational structures.

Towards an understanding of the molecular mechanisms regulating gene expression during diploidization in phylogenetically polyploid lower vertebrates

Polyploidization and regional gene duplication have occurred frequently during vertebrate evolution, providing the genetic material necessary for creating evolutionary novelties. Mammals, including man, can be regarded as diploid species with a polyploid history of evolution. Polyploidization steps during the phylogeny of mammals probably took place in the genomes of amphibian- or fish-like mammalian ancestors. The polyploid status has subsequently been shaped by the process of diploidization, leading to genomes that are polyploid with respect to the amount of genetic material and the number of gene copies, and diploid with respect to the level of gene expression and chromosomal characteristics. Phylogenetically tetraploid amphibian and teleost species together with their diploid close relatives can be used as a model system to study the effect of polyploidization and the mechanisms of diploidization of a parallel event during early mammalian evolution. Experimental evidence permits the assumption that the diploidization of gene expression in tetraploid cyprinid fish may be functionally correlated with structural modifications of the ribosomal components, RNA and protein. These findings are discussed in the light of reduced protein synthesis in diploidized tetraploid species and a mechanism to explain diploidization during mammalian evolution.

Selfish DNA: the ultimate parasite

The DNA of higher organisms usually falls into two classes, one specific and the other comparatively nonspecific. It seems plausible that most of the latter originates by the spreading of sequences which had little or no effect on the phenotype. We examine this idea from the point of view of the natural selection of preferred replicators within the genome.

CELL SIZE, NUCLEAR SIZE AND DNA CONTENT RELATIONSHIPS IN GOSSYPIUM

Cell and nuclear volumes were determined for 17 species and plant types in the genus Gossypium. All species and types, except one, showed a significant positive association between nuclear and cell volume. The overall species r-value (0.694) for cell and nuclear volume is highly significant and positive. For the 17 plant forms, the r-values for association of DNA content and nuclear volume and for association of DNA content and cell volume are 0.625 and 0.655, respectively, and both are highly significant.

Gene action in fish of tetraploid origin. I. Cellular and biochemical parameters in cyprinid fish

In phylogenetically diploid and tetraploid Cyprinid fish species, erythrocyte volumes, protein contents, and mean activities of the enzymes LDH, 6PGD, and PGI per cell per active gene locus decline with increasing DNA contents. These findings are assumed to reflect an evolutionary tendency of polyploids to regulate their genic activity down to the level of the diploids.