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PubMed1993

[A mathematical model for the dynamics of primitive biological macromolecules and its evolutionary implications].

A mathematical model, adopted from the logistic equations for population growth and interspecific competition in ecology, was proposed for the dynamics of primitive biological macromolecules: [formula: see text] where Nm is the copy number of a kind of biological macromolecule in primitive environment at time t. rm is the intrinsic replicating capacity (rate) of the macromolecule. Km is the carrying capacity (resource limit) of the primitive environment. dNm/dt is the instantaneous rate of increase of copy number of the primitive biological macromolecule beta 12 and beta 21 are competition coefficients concerning the inhibition of macromolecule 2 on macromolecule 1 (beta 12), and macromolecule 1 on macromolecule 2 (beta 21) other lower indexes in the equations refer to macromolecule 1 or 2. By analysing the possible competition outcomes deduced from the model, a conclusion with evolutionary implications could be drawn that the biological diversity would be very low shortly after the origin of life in the primitive biosphere. In other words, the abundant biological macromolecules capable of replicating in the primitive biosphere would be quite unique in kinds, and this uniqueness would therefore be the initial basis of biological evolution which would then go from low biological diversity to high biological diversity. The model is also helpful for the understanding of the origin of repeated sequences which are widely present in the genomes of modern organisms.

Animals↗
PubMed1991

Elements in microbial evolution.

Spontaneous mutation, selection, and isolation are key elements in biological evolution. Molecular genetic approaches reveal a multitude of different mechanisms by which spontaneous mutants arise. Many of these mechanisms depend on enzymes, which often do not act fully at random on the DNA, although a large number of sites of action can be observed. Of particular interest in this respect are DNA rearrangement processes, e.g., by transposition and by site-specific recombination systems. The development of gene functions has thus to be seen as the result of both DNA rearrangement processes and sequence alterations brought about by nucleotide substitutions and small local deletions, insertions, and duplications. Prokaryotic microorganisms are particularly appropriate for studying the effects of spontaneous mutation and thus microbial evolution, as they have haploid genomes, so that genetic alterations become rapidly apparent phenotypically. In addition, bacteria and their viruses and plasmids have relatively small genomes and short generation times, which also facilitate research on evolutionary processes. Besides the strategy of development of gene functions in the vertical transmission of genomes from generation to generation, the acquisition of short DNA segments from other organisms appears to be an important strategy in microbial evolution. In this process of horizontal evolution natural vector DNA molecules are often involved. Because of acquisition barriers, the acquisition strategy works best for relatively small DNA segments, hence at the level of domains, single genes, or at most operons. Among the many enzymes and functional systems involved in vertical and horizontal microbial evolution, some may serve primarily for essential life functions in each individual and only secondarily contribute to evolution.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed2005

Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution.

MOTIVATION: We are interested in studying the evolution of DNA single nucleotide polymorphism sequences which have undergone (meiotic) recombination. For a given set of sequences, computing the minimum number of recombinations needed to explain the sequences (with one mutation per site) is a standard question of interest, but it has been shown to be NP-hard, and previous algorithms that compute it exactly work either only on very small datasets or on problems with special structure. RESULTS: In this paper, we present efficient, practical methods for computing both upper and lower bounds on the minimum number of needed recombinations, and for constructing evolutionary histories that explain the input sequences. We study in detail the efficiency and accuracy of these algorithms on both simulated and real data sets. The algorithms produce very close upper and lower bounds, which match exactly in a surprisingly wide range of data. Thus, with the use of new, very effective lower bounding methods and an efficient algorithm for computing upper bounds, this approach allows the efficient, exact computation of the minimum number of needed recombinations, with high frequency in a large range of data. When upper and lower bounds match, evolutionary histories found by our algorithm correspond to the most parsimonious histories. AVAILABILITY: HapBound and SHRUB, programs implementing the new algorithms discussed in this paper, are available at http://wwwcsif.cs.ucdavis.edu/~gusfield/lu.html

Algorithms↗
PubMed2004

Phylogenetics of artificial manuscripts.

Biological evolution has parallels with the development of natural languages, man-made artifacts, and manuscript texts. As a result, phylogenetic methods developed for evolutionary biology are increasingly being used in linguistics, anthropology, archaeology, and textual criticism. Despite this popularity, there have been few critical tests of their suitability. Here, we apply phylogenetic methods to artificial manuscripts with a known true phylogeny, produced by modern 'scribes'. Although the survival of ancestral forms and multiple descendants from a single ancestor are probably much more common in manuscript evolution than biological evolution, we were able to reconstruct most of the true phylogeny. This is important because phylogenetic methods are influencing the production of critical editions of major written works. We also show that the variation in rates of change at different locations in the text follows a gamma distribution, as is often the case in DNA sequences.

Language↗
PubMedDate not supplied

[The nineteenth century roots of the contemporary biological revolution].

The recent publication of the human genomic sequence is the most important progress in biology. It originates from four major watersheds between 1860-1865, namely the biological evolution by Darwin in 1858, the Mendel laws of heredity in 1865, the basis of physiology established by Claude Bernard also in 1865, and the discoveries of microbacteria by Louis Pasteur around 1857. Before 1860, biology did not exist as a science. After 1860, the Darwin's theory progressively became a law after the discovery of the DNA polymorphism and that of the mechanisms of genetic mixing. So far the Mendel's laws were confirmed in parallel with the development of molecular genetics after the discovery of DNA structure and genetic code. The discovery of hormones is one example, amongst several on how integrative physiology applies to Claude Bernard's basis. Finally, based on Pasteur's discovery and Pasteur Institutes, microbiology became a tool for molecular biologists.

Biological Evolution↗
PubMed2004

Public information: from nosy neighbors to cultural evolution.

Psychologists, economists, and advertising moguls have long known that human decision-making is strongly influenced by the behavior of others. A rapidly accumulating body of evidence suggests that the same is true in animals. Individuals can use information arising from cues inadvertently produced by the behavior of other individuals with similar requirements. Many of these cues provide public information about the quality of alternatives. The use of public information is taxonomically widespread and can enhance fitness. Public information can lead to cultural evolution, which we suggest may then affect biological evolution.

Animals↗
PubMed2005

Insights on biology and evolution from microbial genome sequencing.

No field of research has embraced and applied genomic technology more than the field of microbiology. Comparative analysis of nearly 300 microbial species has demonstrated that the microbial genome is a dynamic entity shaped by multiple forces. Microbial genomics has provided a foundation for a broad range of applications, from understanding basic biological processes, host-pathogen interactions, and protein-protein interactions, to discovering DNA variations that can be used in genotyping or forensic analyses, the design of novel antimicrobial compounds and vaccines, and the engineering of microbes for industrial applications. Most recently, metagenomics approaches are allowing us to begin to probe complex microbial communities for the first time, and they hold great promise in helping to unravel the relationships between microbial species.

DNA, Bacterial↗
PubMed1983

The Ernst W. Bertner Memorial Award lecture: the evolution of biological heterogeneity in metastatic neoplasms.

The complexity of the processes of tumor progression and metastasis makes it difficult to provide generalized rules. Results and hypotheses that are based upon a single tumor system or a simple experimental technique are likely to be revised as more data become available. However, bearing these limitations in mind and ignoring the above warnings, I wish to conclude the following: By the time of diagnosis, many malignant neoplasms are heterogeneous, i.e., they contain subpopulations of cells with different biological characteristics. The process of metastasis involves a sequence of complex events whose outcome depends on tumor cell properties and host factors. The metastatic process selects variants from a heterogeneous starting population. The diversity for the metastatic phenotype may be a consequence of the multicellular origin of a neoplasm or it may be the result of continuous evolution and progression in tumors of unicellular origin. Metastatic clones appear, in general, to be less stable than nonmetastatic clones. Metastatic clones exhibit an increased rate of spontaneous mutation compared with nonmetastatic clones. Some metastases may be clonal in their origin, and multiple metastases can originate from different progenitor cells. Biological diversity can rapidly develop within individual metastases. The acquisition of phenotypic heterogeneity by populations of tumor cells imposes a degree of stability on the tumor as a whole. The generation of biological diversity in malignant neoplasms and within and among metastases has profound implications both for studies on the pathogenesis of cancer metastasis and for the design of any successful approach to the treatment of this disease.

Animals↗
PubMed1999

Emergence of homeostasis and "noise imprinting" in an evolution model.

Homeostasis, the creation of a stabilized internal milieu, is ubiquitous in biological evolution, despite the entropic cost of excluding noise information from a region. The advantages of stability seem self evident, but the alternatives are not so clear. This issue was studied by means of numerical experiments on a simple evolution model: a population of Boolean network "organisms" selected for performance of a curve-fitting task while subjected to noise. During evolution, noise sensitivity increased with fitness. Noise exclusion evolved spontaneously, but only if the noise was sufficiently unpredictable. Noise that was limited to one or a few stereotyped patterns caused symmetry breaking that prevented noise exclusion. Instead, the organisms incorporated the noise into their function at little cost in ultimate fitness and became totally noise dependent. This "noise imprinting" suggests caution when interpreting apparent adaptations seen in nature. If the noise was totally random from generation to generation, noise exclusion evolved reliably and irreversibly, but if the noise was correlated over several generations, maladaptive selection of noise-dependent traits could reverse noise exclusion, with catastrophic effect on population fitness. Noise entering the selection process rather than the organism had a different effect: adaptive evolution was totally abolished above a critical noise amplitude, in a manner resembling a thermodynamic phase transition. Evolutionary adaptation to noise involves the creation of a subsystem screened from noise information but increasingly vulnerable to its effects. Similar considerations may apply to information channeling in human cultural evolution.

Algorithms↗
PubMed1995

Low environmental radiation background impairs biological defence of the yeast Saccharomyces cerevisiae to chemical radiomimetic agents.

Background radiation is likely to constitute one of the factors involved in biological evolution since radiations are able to affect biological processes. Therefore, it is possible to hypothesize that organisms are adapted to environmental background radiation and that this adaptation could increase their ability to respond to the harmful effects of ionizing radiations. In fact, adaptive responses to alkylating agents and to low doses of ionizing radiation have been found in many organisms. In order to test for effects of adaptation, cell susceptibility to treatments with high doses of radiomimetic chemical agents has been studied by growing them in a reduced environmental radiation background. The experiment has been performed by culturing yeast cells (Saccharomyces cerevisiae D7) in parallel in a standard background environment and in the underground Gran Sasso National Laboratory, with reduced environmental background radiation. After a conditioning period, yeast cells were exposed to recombinogenic doses of methyl methanesulfonate. The yeast cells grown in the Gran Sasso Laboratory showed a higher frequency of radiomimetic induced recombination as compared to those grown in the standard environment. This suggests that environmental radiation may act as a conditioning agent.

Background Radiation↗
PubMed2003

Biphasic constitutive laws for biological interface evolution.

A model of tissue differentiation at the bone-implant interface is proposed. The basic hypothesis of the model is that the mechanical environment determines the tissue differentiation. The stimulus chosen is related to the bone-implant micromotions. Equations governing the evolution of the interfacial tissue are proposed and combined with a finite element code to determine the evolution of the fibrous tissue around prostheses. The model is applied to the case of an idealized hip prosthesis.

Algorithms↗
PubMed2000

Kinetochore reproduction in animal evolution: cell biological explanation of karyotypic fission theory.

Karyotypic fission theory of Todd offers an explanation for the diverse range of diploid numbers of many mammalian taxa. Theoretically, a full complement of acrocentric chromosomes can be introduced into a population by chromosomal fission. Subsequent inheritance of ancestral chromosomes and paired fission derivatives potentially generates a diploid range from the ancestral condition to double its number of chromosomes. Although it is undisputed that both chromosomal fission and fusion ("Robertsonian rearrangements") have significantly contributed to karyological diversity, it is generally assumed that independent events, the fission of single chromosomes or the fusion of two chromosomes, are the sources of such change. The karyotypic fission idea by contrast posits that all mediocentric chromosomes simultaneously fission. Here I propose a specific cell biological mechanism for Todd's karyotypic fission concept, "kinetochore reproduction theory," where a complete set of dicentric chromatids is synthesized during gametogenesis, and kinetochore protein dephosphorylation regulates dicentric chromatid segregation. Three postulates of kinetochore reproduction theory are: (i) breakage of dicentric chromosomes between centromere pairs forms acrocentric derivatives, (ii) de novo capping of newly synthesized acrocentric ends with telomeric DNA stabilizes these derivatives, and (iii) mitotic checkpoints regulate chromosomal disjunction to generate fissioned karyotypes. Subsequent chromosomal rearrangement, especially pericentric inversion, increases the probability of genetic isolation amongst incipient sympatric species polytypic for fission-generated acrocentric autosomes. This mechanism obviates the requirement for numerous independent Robertsonian rearrangements and neatly accounts for mammalian karyotype evolution as exemplified in analyses of Carnivora, Artiodactyla, and Primates.

Animals↗
PubMed1991

Four analogies between biological and cultural/linguistic evolution.

The intricate phenomena of biology on the one hand, and language and culture on the other, have inspired many writers to draw analogies between these two evolutionary systems. These analogies can be divided into four principal types: species/language, organism/concept, genes/culture, and cell/person. Here, it is argued that the last analogy--between cells and persons--is the most profound in several respects, and, more importantly, can be used to generate a number of empirical predictions. In the first half of the paper, the four analogies are each evaluated after briefly describing criteria for a good predictive analogy. In the second half of the paper, the cell/person analogy and predictions deriving from it are explored in detail.

Biological Evolution↗
PubMedDate not supplied

The early atmosphere: a new picture.

Over the last several years, many of the fundamental ideas concerning the composition and chemical evolution of the Earth's early atmosphere have changed. While many aspects of this subject are clouded--either uncertain or unknown, a new picture is emerging. We are just beginning to understand how astronomical, geochemical, and atmospheric processes each contributed to the development of the gaseous envelope around the third planet from the sun some 4.6 billion years ago and how that envelope chemically evolved over the history of our planet. Simple compounds in that gaseous envelope, energized by atmospheric lightning and/or solar ultraviolet radiation, formed molecules of increasing complexity that eventually evolved into the first living systems on our planet. This process is called "chemical evolution" and immediately preceded biological evolution; once life developed and evolved, it began to alter the chemical composition of the atmosphere that provided the very essence of its creation. Photosynthetic organisms which have the ability to biochemically transform carbon dioxide and water to carbohydrates, which they use for food, produce large amounts of molecular oxygen (O2) as a by-product of the reaction. Atmospheric oxygen photochemically formed ozone, which absorbs ultraviolet radiation from the sun and shields the Earth's surface from this biologically lethal radiation. Once atmospheric ozone levels increased sufficiently, life could leave the safety of the oceans and go ashore for the first time. Throughout the history of our planet, there has been strong interaction between life and the atmosphere. Understanding our cosmic roots is particularly relevant as we embark on a search for life outside the Earth. At this very moment, several radio telescopes around the world are searching for extraterrestrial intelligence (SETI).

Atmosphere↗
PubMed2003

Genomics, evolution and biological functions of the pacifastin peptide family: a conserved serine protease inhibitor family in arthropods.

The last decade, a new serine protease inhibitor family has been described in arthropods. Eight members were purified from the locusts Locusta migratoria (LMPI-1-2 and HI) and Schistocerca gregaria (SGPI-1-5). The light chain of the heterodimeric protease inhibitor pacifastin, from the freshwater crayfish Pacifastacus leniusculus, was found to be composed of nine consecutive inhibitory domains (PLDs). These domains share a pattern of six conserved cysteine residues (Cys-Xaa(9-12)-Cys-Asn-Xaa-Cys-Xaa-Cys-Xaa(2-3)-Gly-Xaa(3-6)-Cys-Thr-Xaa(3)-Cys) with the locust inhibitors. Via cDNA cloning, eight pacifastin-related precursors have been identified in locusts. Interestingly, additional pacifastin-related precursors have been identified in Diptera, Lepidoptera and Coleoptera utilising an in silico data mining approach.

Amino Acid Sequence↗