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PubMed1997

Impact of clonal evolution on the biological diversity of Trypanosoma cruzi.

Trypanosoma cruzi, the agent of Chagas' disease, exhibits considerable biological variability. Moreover, it has been postulated that populations of this protozoan are subdivided into natural clones, which can be separated from each other by considerable levels of evolutionary divergence. The authors have proposed that this long-term clonal evolution may have a profound impact on Trypanosoma cruzi biological diversity. In order to test this hypothesis, 16 T. cruzi stocks representing 3 major clonal genotypes of the parasite were analysed for 8 different in vitro biological parameters. The overall results show a strong statistical linkage between genetic and biological differences. This is in agreement with the working hypothesis, although a notable biological variability is observable among the stocks of each of the 3 major clonal genotypes. The authors propose that T cruzi genetic variability must be taken into account in any applied study dealing with this parasite.

Alleles↗
PubMed2002

A general frame of theory on genetic load.

Genetic load expresses the loss in mean fitness of a population because of the genetic variability present. The quantitative discussion of various genetic loads is provided with important meaning for research into evolution of species on realistic level. The past theory on genetic load starts off with equilibrium of population to investigate the evolution of species on realistic level. However, the evolution is a displacement on equilibrium of population. This is just made up of a contradiction between theory and praxis. We branch out the past theory on genetic load, and give out a general theoretic frame describing the various genetic loads. By the use of this theoretic frame the genetic loads in an equilibrium population can be represented, and the genetic loads in a non-equilibrium population and their change can also be simulated. Thus this theoretic frame overcomes the shortcoming of past theory on genetic loads, which can't describe non-equilibrium population and conflicts with praxis of biological evolution sometimes, and offers a sort of credible simulation methods for research into evolution of species.

Genetic Load↗
PubMed2005

Canalizing Kauffman networks: nonergodicity and its effect on their critical behavior.

Boolean networks have been used to study numerous phenomena, including gene regulation, neural networks, social interactions, and biological evolution. Here, we propose a general method for determining the critical behavior of Boolean systems built from arbitrary ensembles of Boolean functions. In particular, we solve the critical condition for systems of units operating according to canalizing functions and present strong numerical evidence that our approach correctly predicts the phase transition from order to chaos in such systems.

Biophysics↗
PubMed2003

Photoelectrochemical power, chemical energy and catalytic activity for organic evolution on natural pyrite interfaces.

Natural pyrite (FeS2) has frequently been discussed as a material involved in CO2 fixation in presence of H2S and as a possible catalyst for the origin of life. A straightforward chemical fixation of carbon dioxide as proposed by Wächtershauser could not be verified from thermo-chemical equilibrium calculations by minimizing Gibb's Free Energy in the system C, O, H, S, Fe and appears unlikely due to the experimentally encountered large overpotentials involved in CO2 fixation. However, the hypothesis, by W. R. Edwards, that pyrite in shallow coastal waters may have been involved, can be sustained. In this case, daily available photoelectrochemical power from FeS2/Fe2+/3+ interfaces could have made the difference in combination with electrochemical processes, such as hydrogen insertion, and the solubilization of pyrite by the amino acid cysteine to yield dissolved chemical energy. Periodical changes in energy supply could also have entrained primitive self-organization processes for organic-biological evolution. Natural samples from thirteen ore deposits have been investigated photoelectrochemically. Efficient light-induced current generation has been found with several of these samples so that photoelectrochemical processes generated by pyrite have to be considered as naturally occurring phenomena, which could have been even more pronounced in oxygen deficient environments. Pyrite from the Murgul mine in Turkey of suboceanic volcanic origin was closer examined as a model system to understand the morphology and chemistry of pyrite photoactivity.

Carbon Dioxide↗
PubMed1987

Variation of efficiency with free-energy dissipation in models of biological energy transduction.

For two models of biological free-energy transducers, it is investigated how free-energy dissipation and efficiency vary as (i) the demand for output free energy, (ii) the input free energy or (iii) the properties of the transducers themselves, are varied. One model is representative of near-equilibrium free-energy transducers in general, the other is a special case of far-from-equilibrium free-energy transduction, reminiscent of proton pumping by bacteriorhodopsin. It turns out that the relationship between efficiency and free-energy dissipation depends strongly on what varies. In some cases, free-energy dissipation increases as the efficiency increases. It is suggested that this is one reason why biological evolution has not resulted in high efficiencies and low rates of free-energy dissipation. For the near-equilibrium free-energy transducer, the free-energy dissipation at the static head steady state is minimal with respect to variations in the output force. For the far-from-equilibrium model (of bacteriorhodopsin), the static head does not correspond to such a minimum, if that free-energy transducer slips.

Bacteriorhodopsins↗
PubMed2005

An algorithm for linear metabolic pathway alignment.

Metabolic pathway alignment represents one of the most powerful tools for comparative analysis of metabolism. It involves recognition of metabolites common to a set of functionally-related metabolic pathways, interpretation of biological evolution processes and determination of alternative metabolic pathways. Moreover, it is of assistance in function prediction and metabolism modeling. Although research on genomic sequence alignment is extensive, the problem of aligning metabolic pathways has received less attention. We are motivated to develop an algorithm of metabolic pathway alignment to reveal the similarities between metabolic pathways. A new definition of the metabolic pathway is introduced. The algorithm has been implemented into the PathAligner system; its web-based interface is available at http://bibiserv.techfak.uni-bielefeld.de/pathaligner/.

Algorithms↗
PubMed2004

How independent are the appearances of n-mers in different genomes?

MOTIVATION: Analysis of statistical properties of DNA sequences is important for evolutional biology as well as for DNA probe and PCR technologies. These technologies, in turn, can be used for organism identification, which implies applications in the diagnosis of infectious diseases, environmental studies, etc. RESULTS: We present results of the correlation analysis of distributions of the presence/absence of short nucleotide subsequences of different length ('n-mers', n = 5-20) in more than 1500 microbial and virus genomes, together with five genomes of multicellular organisms (including human). We calculate whether a given n-mer is present or absent (frequency of presence) in a given genome, which is not the usually calculated number of appearances of n-mers in one or more genomes (frequency of appearance). For organisms that are not close relatives of each other, the presence/absence of different 7-20mers in their genomes are not correlated. For close biological relatives, some correlation of the presence of n-mers in this range appears, but is not as strong as expected. Suppressed correlations among the n-mers present in different genomes leads to the possibility of using random sets of n-mers (with appropriately chosen n) to discriminate genomes of different organisms and possibly individual genomes of the same species including human with a low probability of error.

Algorithms↗
PubMed2003

PaTre: a method for paralogy trees construction.

Genomes can be described as a collection of clusters, the gene families, whose members are called paralogs. Paralogs are genes that most probably share duplication history and show a significant similarity in their sequences, even if they perform slightly different biological function. Among the different mechanisms that have led to an increase of the genomic information during biological evolution, gene duplication is probably the most important. To better understand duplication events, the first step is to investigate the history of the gene families in order to detect which duplication events have taken place, and in which relative (partial) order. Here we present a method, called PaTre, that, given a gene family, attempts to construct the paralogy tree of the family. We will work under the hypothesis that every family member derives from a duplication process of another member. By the term paralogy tree, we mean a directed tree in which the root represents the most ancient paralog of the family and each oriented arc (a, b) represents the existence of a duplication event from the template gene a to its copy b. Notice that gene a survives the event and can serve as a template of more than one duplication event; in fact, there can be more than one arc leaving a. PaTre uses new algorithmic techniques motivated by the specific application at hand. The reliability of the inferential process has been tested by means of a simulator that implements different hypotheses on the duplication-with-modification paradigm and on three examples of different biological gene families, belonging either to lower and higher organisms.

Arabidopsis↗
PubMed1985

Origins of life: conformational energy calculations on primitive tRNA nestling an amino acid.

We report conformational energy calculations on our proposal of a molecular interaction theory for the origin of the nucleic acid-directed, adaptor-mediated synthesis of proteins that links the phenomena of chemical and biological evolution. A particular conformation of a pentanucleotide turns out to be a double-sided template for a primitive decoding system. It is able to neatly nestle an amino acid via hydrogen bonds, and this complex is found to be an energetically favourable conformation. The total potential energy of the complex is calculated using semi-empirical potential energy functions. A local-minimum conformation is obtained and its features are reported. The template conformation of the pentanucleotide is found to have an energy value far lower than a regular helical conformation. When the amino acid is nestled in the cleft of the template-conformation through specific hydrogen bonds, the energy is further lowered. A D-amino acid nestled into the PIT (Primitive tRNA) is found to be less stable than its L counterpart, as revealed by energy calculations.

Amino Acids↗
PubMed2005

Phase transition in random catalytic networks.

The notion of (auto)catalytic networks has become a cornerstone in understanding the possibility of a sudden dramatic increase of diversity in biological evolution as well as in the evolution of social and economical systems. Here we study catalytic random networks with respect to the final outcome diversity of products. We show that an analytical treatment of this long-standing problem is possible by mapping the problem onto a set of nonlinear recurrence equations. The solution of these equations shows a crucial dependence of the final number of products on the initial number of products and the density of catalytic production rules. For a fixed density of rules we can demonstrate the existence of a phase transition from a practically unpopulated regime to a fully populated and diverse one. The order parameter is the number of final products. We are able to fully understand the origin of this phase transition as a crossover from one set of solutions from a quadratic equation to the other. We observe a remarkable similarity of the solution of the system and the PVT diagrams in standard thermodynamics.

Algorithms↗
PubMed1997

Sound emission from cochlear filters and foveae--does the auditory sense organ make sense?

Sense organs filter relevant information from a broad background of physical interactions and discard possible perceptual input that has not proven useful during the course of biological evolution. Sense organs not only limit the access to physical reality, under certain conditions they have a life of their own and produce responses even in the absence of physical stimulation. As a perfect example, the inner ear, the cochlea, in addition to detecting incoming sound waves, it also is capable of producing sound energy. Such "active" processes, however, seem to be necessary to push detection thresholds close to physical limits. The price that has to be paid are "cochlear artifacts" like otoacoustic emissions. In the following, measurement of sound that is emitted by the ear will be introduced as a noninvasive means to assess cochlear function and to help to unravel the mechanical interaction between sensory cells and supporting structures that ultimately leads to sensitive and sharply tuned auditory perception. One focus will be on the cochlea of echo-locating bats that use audition as the main window of perception to their environment and therefore have highest demands on cochlear performance.

Animals↗
PubMed2004

Parallels in invasion and angiogenesis provide pivotal points for therapeutic intervention.

Biological evolution is economical and successful fundamental processes are frequently recapitulated. There are remarkable similarities in the molecular mechanisms which enable tumour cells to invade into surrounding tissues and activated endothelial cells to generate new capillaries, which facilitate the growth and dissemination of cancer. Indeed these pathological processes are themselves based upon key vertebrate developmental processes, and in some cases parallel strategies used by microorganisms to colonise their hosts' tissues. The aim of this review is to explore these parallels in more detail and indicate possible pivotal points for therapeutic intervention. These novel approaches may ultimately optimise the selective targeting of processes involved in tumour invasion and angiogenesis, while sparing normal adult proliferating tissues. Strategies include inhibition of oncogenic pathways in tumour cells which not only stimulate tumour cell growth and invasion, but also initiate neoangiogenesis by upregulation of angiogenic cytokines. Secondly, downstream signalling pathways, transcriptional regulation and effectors common to both processes, and finally points of interaction/cross-talk between tumour cells and endothelial cells which are necessary to enable invasion and angiogenesis to proceed.

Animals↗
PubMed2007

Four hypotheses on mitochondria's role in the development and regulation of oxidative stress in the normal state, cell pathology and reversion of tumor cells.

The biological evolution has resulted in adaptation of both unicellular and multicellular organisms to negative effect of excessive O2 in reply to gradual increase of free oxygen (O2) contents in the earth atmosphere. This adaptation has led to formation of various antioxidant systems in the organism. Such system within the cell has hierarchic structure and is represented by at least than three levels of protection: antioxygene, antiradical and antiperoxide. The first and most effective antioxidant level is represented as mitochondrial respiration able to perform several functions. One of these functions is antioxygene since the very the mitochondria's capability to be a main O2 consumer in the cell provides for low but sufficient for respiration and energy supply levels of O2 partial pressure and dependent concentrations of active O2 forms. The latters, being signal molecules at certain values, modify regular and synthetic processes in the cells either directly or indirectly. This is the possibility for mitochondria to more extensively affect the intracellular processes than simply produce ATP. In case of defective of the cell first protection line the hyperoxia starts due to poor utilization of the incoming O2. Change in mitochondria's "capacity" (quantity, size and maturity level of mitochondria) anyway occurring in the cells are an efficient way of regulation of the oxy-peroxide condition (oxidative stress) and related signal channels. The relationship between changes in the condition of cells, i.e. from their normal state to different pathologic forms, and growing disbalance Delta(PO-AO) between its pro-oxygen (PO) and anti-oxygen (AO) components has been assumed. It is expected that during the evolution the cell could have supposedly acquired a sequence of "specialized" Delta(PO-AO) disbalances. Each sequence needs to implement a certain set of biochemical processes. The probability of Delta(PO-AO) disbalance gradation with specification of their value ranges has been determined. These ranges identify or impact certain cell state, namely proliferation of normal cell (oxidative mitogenesis), ageing, A1 apoptosis, carcinogenesis, A2 apoptosis, and oxidative cytolysis. The cited assumption allows us to: (1) explain reverse dependence of cell proliferation due to the level of their differentiation, increase in the amount and activity of mitochondria as an indispensable condition for the disbalance shift towards differentiation, (2) bring up the idea that regress of the cells, and in particular tumour cells, directly results from the Delta(PO-AO) disbalance decrease to certain levels under the influence of reverse inductors, (3) explain relatively easy and frequent embryonic and stem cells malignancy, and also their reversal normalization. These phenomena occur due to small number and/or size of mitochondria in the designated cells. To verify the above mentioned hypotheses it is primarily necessary to be able to stimulate and slow down the mitochondria biogenesis in the embryonic, stem, ageing, cancer and other cells.

Animals↗
PubMed2006

'Universal' microstructural patterns in cortical and trabecular, extracellular and extravascular bone materials: micromechanics-based prediction of anisotropic elasticity.

Bone materials are characterized by an astonishing variability and diversity. Still, because of 'architectural constraints' due to once chosen material constituents and their physical interaction, the fundamental hierarchical organization or basic building plans of bone materials remain largely unchanged during biological evolution. Such universal patterns of microstructural organization govern the mechanical interaction of the elementary components of bone (hydroxyapatite, collagen, water; with directly measurable tissue-independent elastic properties), which are here quantified through a multiscale homogenization scheme delivering effective elastic properties of bone materials: at a scale of 10nm, long cylindrical collagen molecules, attached to each other at their ends by approximately 1.5nm long crosslinks and hosting intermolecular water inbetween, form a contiguous matrix called wet collagen. At a scale of several hundred nanometers, wet collagen and mineral crystal agglomerations interpenetrate each other, forming the mineralized fibril. At a scale of 5-10microm, the extracellular solid bone matrix is represented as collagen fibril inclusions embedded in a foam of largely disordered (extrafibrillar) mineral crystals. At a scale above the ultrastructure, where lacunae are embedded in extracellular bone matrix, the extravascular bone material is observed. Model estimates predicted from tissue-specific composition data gained from a multitude of chemical and physical tests agree remarkably well with corresponding acoustic stiffness experiments across a variety of cortical and trabecular, extracellular and extravascular materials. Besides from reconciling the well-documented, seemingly opposed concepts of 'mineral-reinforced collagen matrix' and 'collagen-reinforced mineral matrix' for bone ultrastructure, this approach opens new possibilities in the exploitation of computer tomographic data for nano-to-macro mechanics of bone organs.

Animals↗
PubMed1981

Estradiol receptor-binding protein in head and neck neoplastic and normal tissue.

Estradiol (E2) receptor-binding protein was measured in 42 neoplasms and normal tissues from the head and neck region. Tissues with high E2 receptor protein content included normal skin and normal mucosa of the nose and the floor of the mouth and of the parotid and submandibular salivary glands. Two of four papillary carcinomas of the thyroid, three of five pleomorphic adenomas of the parotid, four of six squamous cell carcinomas of the oral cavity, one of angiofibroma of the nose, and an eye (sclera) melanoma also had a high content of E2-binding protein. The demonstration of estrogen receptors in these neoplasms may indicate that these tumors also, as many breast lesions, may be hormone-dependent. If this is correct, an appropriate hormonal treatment may influence their biological evolution.

Adenoma↗
PubMed2000

The shape of life: how much is written in stone?

Considering the enormous diversity of living organisms, representing mostly untapped resources for studying ecological, ontogenetic and phylogenetic patterns and processes, why should evolutionary biologists concern themselves with the remains of animals and plants that died out tens or even hundreds of millions of years ago? The reason is that important new insights into some of the most vexing evolutionary questions are being revealed at the interfaces of palaeontology, developmental biology and molecular biology. Attempts to synthesise information from these disciplines, however, often encounter their greatest hurdles in considerations of the radiation of the Metazoa. Ongoing challenges relate to the origins of body plans, the relationships of the metazoan phyla and the timing of major evolutionary radiations. Palaeontology not only has its own unique contributions to the study of evolutionary processes, but provides a lynchpin for many of the emerging techniques.

Animals↗