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PubMed2006

Needle enzyme electrode based glucose diffusive transport measurement in a collagen gel and validation of a simulation model.

Rapid response needle enzyme electrodes were fabricated to measure the glucose concentration at the centre of a cylindrical spiralled collagen gel, which is a relevant constituent for tissue engineering scaffolds. The experimental data were based on a low consumption glucose sensor which minimised the distorting effect of enzymatic degradation. As the measurement was carried out within a collagen gel the stirring independence was compulsory for the biosensor. Glucose concentration changes were derived from a model based on the solution to Fick's Second Law. This had two different expressions for different dimensionless time (T) domains. The expression for large T and a first order approximation for small T were known. The expression for high order approximation for small T was then derived. An analytical expression consisting of fast convergent parts of these two expressions is proposed, which operates for the entire time region. A computational model for glucose concentration evolution where an electrode is located is proposed to operate for extended time periods. The model was confirmed by agreement between the simulated and observed data. An experimental technique is developed here to determine glucose diffusion coefficient by fitting the simulated concentration profile to the observed one. The glucose diffusion coefficient within the collagen gel was estimated to be 1.3 x 10(-6) cm(2) s(-1); higher accuracy is achieved here because errors due to noise, baseline and zero time determination are minimised with best fit.

Biosensing Techniques↗
PubMed2002

Caring science and the science of unitary human beings: a trans-theoretical discourse for nursing knowledge development.

BACKGROUND: Two dominant discourses in contemporary nursing theory and knowledge development have evolved over the past few decades, in part by unitary science views and caring theories. Rogers' science of unitary human beings (SUHB) represents the unitary directions in nursing. Caring theories and related caring science (CS) scholarship represent the other. These two contemporary initiatives have generated two parallel, often controversial, seemingly separate and unrelated, trees of knowledge for nursing science. AIM: This paper explores the evolution of CS and its intersection with SUHB that have emerged in contemporary nursing literature. We present a case for integration, convergence, and creative synthesis of CS with SUHB. A trans-theoretical, trans-disciplinary context emerges, allowing nursing to sustain its caring ethic and ontology, within a unitary science. METHODS: The authors critique and review the seminal, critical issues that have separated contemporary knowledge developments in CS and SUHB. Foundational issues of CS, and Watson's theory of transpersonal caring science (TCS), as a specific exemplar, are analysed, alongside parallel themes in SUHB. By examining hidden ethical-ontological and paradigmatic commonalities, trans-theoretical themes and connections are explored and revealed between TCS and SUHB. CONCLUSIONS: Through a creative synthesis of TCS and SUHB we explicate a distinct unitary view of human with a relational caring ontology and ethic that informs nursing as well as other sciences. The result: is a trans-theoretical, trans-disciplinary view for nursing knowledge development. Nursing's history has been to examine theoretical differences rather than commonalities. This trans-theoretical position moves nursing toward theoretical integration and creative synthesis, vs. separation, away from the 'Balkanization' of different theories. This initiative still maintains the integrity of different theories, while facilitating and inviting a new discourse for nursing science. The result: Unitary Caring Science that evokes both science and spirit.

Consciousness↗
PubMed2006

Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics.

BACKGROUND: Vertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebrates, including lampreys, teleosts, amphibians, reptiles, birds, and mammals. The SWS1 genes exhibit many of the characteristics of genes typically targeted for phylogenetic analyses. This study investigates both the utility of SWS1 as a marker for inferring vertebrate phylogenetic relationships, and the characteristics of the gene that contribute to its phylogenetic utility. RESULTS: Phylogenetic analyses of vertebrate SWS1 genes produced topologies that were remarkably congruent with generally accepted hypotheses of vertebrate evolution at both higher and lower taxonomic levels. The few exceptions were generally associated with areas of poor taxonomic sampling, or relationships that have been difficult to resolve using other molecular markers. The SWS1 data set was characterized by a substantial amount of among-site rate variation, and a relatively unskewed substitution rate matrix, even when the data were partitioned into different codon sites and individual taxonomic groups. Although there were nucleotide biases in some groups at third positions, these biases were not convergent across different taxonomic groups. CONCLUSION: Our results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups. This may result from constraints imposed by the functional role of SWS1 pigments in visual transduction.

Animals↗
PubMed2005

Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species.

To explore the role of transcriptome polymorphism in adaptation of organisms to their environment, we evaluated this parameter for the Escherichia coli/Shigella bacterial species, which is composed of well-characterized phylogenetic groups that exhibit characteristic life styles ranging from commensalism to intracellular pathogenicity. Both the genomic content and the transcriptome of 10 strains representative of the major E. coli/Shigella phylogenetic groups were evaluated using macroarrays displaying the 4290 K12-MG1655 open reading frames (ORFs). Although Shigella and enteroinvasive E. coli (EIEC) are not monophyletic, phylogenetic analysis of the binary coded (presence/absence) gene content data showed that these organisms group together due to similar patterns of undetectable K12-MG1655 genes. The variation in transcript abundance was then analyzed using a core genome of 2880 genes present in all strains, after adjusting RNA hybridization signals for DNA hybridization signals. Nonrandom changes in gene expression during the evolution of the E. coli/Shigella species were evidenced. Phylogenetic analysis of transcriptome data again showed that Shigella and EIEC strains group together in terms of gene expression, and this convergence involved groups of genes displaying biologically coherent patterns of functional divergence. Unlike the other E. coli strains evaluated, Shigella and EIEC are intracellular pathogens, and therefore face similar selective pressures. Thus, within the E. coli/Shigella species, strains exhibiting a particular life style have converged toward a specific gene expression pattern in a subset of genes common to the species, revealing the role of selection in shaping transcriptome polymorphism.

Caco-2 Cells↗
PubMed1997

A new symmetrodont mammal from China and its implications for mammalian evolution.

A new symmetrodont mammal has been discovered in the Mesozoic era (Late Jurassic or Early Cretaceous period) of Liaoning Province, China. Archaic therian mammals, including symmetrodonts, are extinct relatives of the living marsupial and placental therians. However, these archaic therians have been mostly documented by fragmentary fossils. This newfossil taxon, represented by a nearly complete postcranial skeleton and a partial skull with dentition, is the best-preserved symmetrodont mammal yet discovered. It provides a new insight into the relationships of the major lineages of mammals and the evolution of the mammalian skeleton. Our analysis suggests that this new taxon represents a part of the early therian radiation before the divergence of living marsupials and placentals; that therians and multituberculates are more closely related to each other than either group is to other mammalian lineages; that archaic therians lacked the more parasagittal posture of the forelimb of most living therian mammals; and that archaic therians, such as symmetrodonts, retained the primitive feature of a finger-like promontorium (possibly with a straight cochlea) of the non-therian mammals. The fully coiled cochlea evolved later in more derived therian mammals, and is therefore convergent to the partially coiled cochlea of monotremes.

Animals↗
PubMed1975

Nuclear characteristics and phylogeny in the protistan phylum Ciliophora.

Ciliates possess a number of nuclear characteristics which, in combination, are unique among the Protista. Nevertheless, attempts to understand the origin - presumably from a flagellate ancestry - of the Ciliophora as a phylum must be made, as well as efforts to elucidate phylogenetic pathways within the large and diverse assemblage represented by its present-day forms. The macronucleus may provide an important clue to early ciliate phylogeny, since we still have, among extant species, groups of distinct "karyological relicts" exhibiting the very features expected in hypothetical forms corresponding to postulated stages in macronuclear origin and evolution. The relationship of the groups of "relict" species to the predominant polyploid-macronucleate forms, with a direct impact on the classification system as well as ciliate evolution and phylogeny in general, is discussed in some detail. Arguments are presented for taxonomic separation of the relatively primitive homokaryotic and diploid-macronucleate forms, which also share other features in common related to their being members of the interstitial fauna, from the more advanced ciliates. The problem is complicated by the non-nuclear structural complexities of these sand-dwelling forms, apparently secondarily-derived specializations which, by convergence, have come to resemble certain non-homologous features of the allegedly more highly evolved groups.

Biological Evolution↗
PubMed1991

Pedigrees of neurobehavioral circuits: tracing the evolution of novel behaviors by comparing motor patterns, muscles, and neurons in members of related taxa.

Comparisons of homologous elements in neurobehavioral circuits that have diverged during speciation to mediate different behaviors should reveal the nature of evolutionary changes in nervous systems. When the pedigree of a particular behavior can be traced-by comparing motor patterns and their neural substrates in related taxa whose phylogeny is known from other (non-neurobehavioral) criteria-divergent and convergent evolutionary changes can be distinguished and the order of their occurrence reconstructed. An example of reconstructing a behavioral pedigree (for the novel mode of swimming in the crab Emerita [Hippidae]) is presented, and implications about the evolution and organization of neurobehavioral circuits engendered by this and some other studies of functionally defined neuronal networks are reviewed. Specific neural differences in related animals can only be attributed to natural selection when they can be related to species differences in function or behavior. Differences that cannot be so related, as well as apparently non-adaptive characters in individual nervous systems, are attributed to ontogenetic processes, which apparently, in some cases, introduced and, in other cases, resisted change through evolutionary time. More expressly-comparative investigations of discrete neurobehavioral circuits are needed for an understanding of the interdependence of evolutionary processes and ontogenetic and functional constraints on the organization of neuronal systems.

Animals↗
PubMed2002

Darwinian selection leads to Gaia.

The Gaia hypothesis, in its strongest form, states that the Earth's atmosphere, oceans, and biota form a tightly coupled system that maintains environmental conditions close to optimal for life. According to Gaia theory, optimal conditions are intrinsic, immutable properties of living organisms. It is assumed that the role of Darwinian selection is to favor organisms that act to stabilize environmental conditions at these optimal levels. In this paper, an alternative form of Gaia theory based on more traditional Darwinian principles is proposed. In the new approach, environmental regulation is a consequence of population dynamics, not Darwinian selection. The role of selection is to favor organisms that are best adapted to prevailing environmental conditions. However, the environment is not a static backdrop for evolution, but is heavily influenced by the presence of living organisms. The resulting co-evolving dynamical process eventually leads to the convergence of equilibrium and optimal conditions. A simple Daisyworld model is used to illustrate this convergence phenomenon. Sensitivity analysis of the Daisyworld model suggests that in stable ecosystems, the convergence of equilibrium and optimal conditions is inevitable, provided there are no externally driven shocks to the system. The end result may appear to be the product of a cooperative venture, but is in fact the outcome of Darwinian selection acting upon "selfish" organisms.

Adaptation, Physiological↗
PubMed1999

Simulation of low-Reynolds-number flow via a time-independent lattice-Boltzmann method.

We present a numerical method to solve the equations for low-Reynolds-number (Stokes) flow in porous media. The method is based on the lattice-Boltzmann approach, but utilizes a direct solution of time-independent equations, rather than the usual temporal evolution to steady state. Its computational efficiency is 1-2 orders of magnitude greater than the conventional lattice-Boltzmann method. The convergence of the permeability of random arrays of spheres has been analyzed as a function of mesh resolution at several different porosities. For sufficiently large spheres, we have found that the convergence is quadratic in the mesh resolution.

Journal Article↗
PubMed2026

Virome-wide ubiquitin ligase discovery reveals diverse mechanisms of immune evasion.

Viruses are intracellular parasites that reprogram the host proteome to promote replication and evade immune recognition. We applied a virome-wide library of ~10,000 open reading frames to discover viral ubiquitin ligases, mapping their mechanisms of degradation and host substrates using targeted CRISPR screens and proteomics. These viral effectors could be classified as canonical ligases that mimic host E3s, hijackers that redirect host E3s, and noncanonical ligases that rewire cullin-RING ligase machinery. These diverse strategies of virus-mediated degradation converged on immune-related substrates, including JAK1 and CUL1β-TrCP, underscoring immune evasion as a major driver of viral ubiquitin ligase evolution. Our findings elucidate viral strategies for exploiting the ubiquitin-proteasome system with potential for therapeutic targeting.

Humans↗
PubMed1998

[Modelling of intraperitoneal chemohyperthermia: experimental study and identification of certain thermal aspects].

Intraperitoneal chemohyperthermia is more and more considered as an interesting therapeutic option in cases of some abdominal cancers, particularly of digestive origin. However, many technical aspects of this treatment remain far from being mastered, particularly the homogeneous dispatch of temperatures within the abdomen cavity. This work consists, first of all, in an experimental study, which is being carried out on a physical "prototype" of the abdomen, on which different hot fluid flows and injection conditions (configurations) are investigated. The results of this experimental study are prospected in two ways. First, an a priori thermal model is proposed, based on physical equations (heat transfer, etc.). Then a "black box" model is identified from the measured temperatures evolutions, so as to obtain a model of the "system" behaviour. Finally, the two modelling approaches are being compared, and the results converge to a simple expression of a few parameters, either physical or identified. These modelling results have helped to optimize the injection circuit and its running parameters while applied to the human treatment.

Algorithms↗
PubMed2003

The geometry of the marmot (rodentia: sciuridae) mandible: phylogeny and patterns of morphological evolution.

Marmots have a prominent role in the study of mammalian social evolution, but only recently has their systematics received the attention it deserves if sociobiological studies are to be placed in a phylogenetic context. Sciurid morphology can be used as model to test the congruence between morphological change and phylogeny because sciurid skeletal characters are considered to be inclined to convergence. However, no morphological study involving all marmot species has ever been undertaken. Geometric morphometric techniques were applied in a comparative study of the marmot mandible. The adults of all 14 living marmot species were compared, and mean mandible shape were used to investigate morphological evolution in the genus Marmota. Three major trends were observed. First, the phylogenetic signal in the variation of landmark geometry, which describes mandible morphology, seems to account for the shape differences at intermediate taxonomic levels. The subgenera Marmota and Petromarmota, recently proposed on the basis of mitochondrial cytochrome b sequence, receive support from mandible morphology. When other sciurid genera were included in the analysis, the monophyly of the genus Marmota and that of the tribe Marmotini (i.e., marmots, prairie dogs, and ground squirrels) was strengthened by the morphological data. Second, the marmotine mandible may have evolved as a mosaic of characters and does not show convergence determined by size similarities. Third, allopatric speciation in peripheral isolates may have acted as a powerful force for modeling shape. This hypothesis is strongly supported by the peculiar mandible of M. vancouverensis and, to a lesser degree, by that of M. olympus, both thought to have originated as isolated populations in Pleistocene ice-free refugia.

Adaptation, Biological↗
PubMed2005

An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences.

BACKGROUND: The concept of a genomic core, defined as the set of genes ubiquitous in all genomes of a monophyletic group, has become crucial in comparative and evolutionary genomics. However, it is still a matter of debate whether lateral gene transfers (LGT) may affect the components of genomic cores, preventing their use to retrace species evolution. We have recently reconstructed the phylogeny of Archaea by using two large concatenated datasets of core proteins involved in translation and transcription, respectively. The resulting trees were largely congruent, showing that informational gene components of the archaeal genomic core belonging to two distinct molecular systems contain a coherent signal for archaeal phylogeny. However, some incongruence remained between the two phylogenies. This may be due either to undetected LGT and/or to a lack of sufficient phylogenetic signal in the datasets. RESULTS: We present evidence strongly favoring of the latter hypothesis. In fact, we have updated our transcription and translation datasets with five new archaeal genomes for a total of 6384 and 2928 amino acid positions, respectively, and 25 taxa. This increase in taxonomic sampling led to the nearly complete convergence of the transcription-based and translation-based trees on a single phylogenetic pattern for archaeal evolution. In fact, only a single incongruence persisted between the two phylogenies. This concerned Methanopyrus kandleri, whose placement remained strongly biased in the transcription tree due to its above average evolutionary rates, and could not be counterbalanced due to the lack of availability of closely related and/or slower-evolving relatives. CONCLUSION: To our knowledge, this is the first report of evidence that the phylogenetic signal harbored by components of the archaeal translation apparatus is confirmed by additional markers belonging to a second molecular system (i.e. transcription). This rules out the risk of circularity when inferring species evolution by small subunit ribosomal RNA and ribosomal protein sequences, since it has been suggested that concerted LGT may affect these markers. Our results strongly support the existence of a core of proteins that has evolved mainly through vertical inheritance in Archaea, and carries a bona fide phylogenetic signal that can be used to retrace the evolutionary history of this domain. The identification and analysis of additional molecular markers not affected by LGT should continue defining the emerging picture of a genuine phylogenetic core for the third domain of life.

Algorithms↗
PubMed2004

A new type of floral oil from Malpighia coccigera (Malpighiaceae) and chemical considerations on the evolution of oil flowers.

New, partially acetylated dihydroxy fatty acids could be identified in the floral oil of Malpighia coccigera (Malpighiaceae): 7-OAc,3-OH 20:0, 7-OAc,3-OH 22:0, 9-OAc,3-OH 22:0, 9-OAc,5-OH 22:0, 3,9-diOAc 22:0, 9-OAc,3-OH 24:0, and 11-OAc,5-OH 24:0. The substitution patterns of all hitherto undescribed dihydroxylated and additionally identified monohydroxylated fatty acids are in agreement with a polyketide analogous biosynthesis. Intermediates may be 3-acetoxy fatty acids (C16, C18, and C20), known from flower secretions of other phylogenetically unrelated plant families. A possible relationship between plant epicuticular wax and floral oil biosynthesis is discussed. It may explain why an independent but convergent development of oil flowers and flower oils in unrelated plant families was possible.

Evolution, Chemical↗
PubMed2000

Heat shock protein 60 sequence comparisons: duplications, lateral transfer, and mitochondrial evolution.

Heat shock proteins 60 (GroEL) are highly expressed essential proteins in eubacterial genomes and in eukaryotic organelles. These chaperone proteins have been advanced as propitious marker sequences for tracing the evolution of mitochondrial (Mt) genomes. Similarities among HSP60 sequences based on significant segment pair alignment calculations are used to deduce associations of sequences taking into account GroEL functional/structural domain differences and to relate HSP60 duplications pervasive in alpha-proteobacterial lineages to the dynamics of lateral transfer and plasmid integration. Multiple alignments with consensuses are determined for 10 natural groups. The group consensuses sharpen the similarity contrasts among individual sequences. In particular, the Mt group matches best with the classical alpha-proteobacteria and closely with Rickettsia but significantly worse with the rickettsial groups Ehrlichia and Orientia. However, across broad protein sequence comparisons, there appears to be no consistent prokaryote whose protein sequences align best with animal Mt genomes. There are plausible scenarios indicating that the nuclear-encoded HSP60 (and HSP70) sequences functioning in Mt are results of lateral transfer and are probably derived from an alpha-proteobacterium. This hypothesis relates to the plethora of duplicated HSP60 sequences among the classical alpha-proteobacteria contrasted with no duplications of HSP60 among other clades of proteobacterial genomes. Evolutionary relations are confounded by differential selection pressures, convergence, variable mutational rates, site variability, and lateral gene transfer.

Bacteria↗
PubMed2000

Do pheromone binding proteins converge in amino acid sequence when pheromones converge?

Convergence in amino acid sequences between proteins can be strong evidence for selection. Here, I look for evidence of convergence in the amino acid sequences of pheromone binding protein (PBP) in response to convergence in pheromones. PBPs are involved in sex pheromone reception by the antennae of male moths. In this role PBPs may selectively bind pheromone components and experience convergent selection in response to convergence in pheromone components. However, examination of the PBPs of the taxa that have converged upon the use of (E)- or (Z)-11-tetradecenyl acetate as their major pheromone component reveals little evidence for convergence in the PBPs identified from these taxa. A few sites show a pattern consistent with convergence or parallelism; however, it cannot be ruled out that these sites share the ancestral state. Two of these sites fall within the proposed binding region of PBPs. These results suggest that PBPs either have not converged in sequence or have converged at very few sites in response to convergence on the same pheromone component.

Amino Acid Sequence↗
PubMed2006

Unpredictability induced by unfocused games in evolutionary game dynamics.

Evolutionary game theory is a basis of replicator systems and has applications ranging from animal behavior and human language to ecosystems and other hierarchical network systems. Most studies in evolutionary game dynamics have focused on a single game, but, in many situations, we see that many games are played simultaneously. We construct a replicator equation with plural games by assuming that a reward of a player is a simple summation of the reward of each game. Even if the numbers of the strategies of the games are different, its dynamics can be described in one replicator equation. We here show that when players play several games at the same time, the fate of a single game cannot be determined without knowing the structures of the whole other games. The most absorbing fact is that even if a single game has a ESS (evolutionary stable strategy), the relative frequencies of strategies in the game does not always converge to the ESS point when other games are played simultaneously.

Animals↗
PubMed1987

A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony.

The method of evolutionary parsimony--or operator invariants--is a technique of nucleic acid sequence analysis related to parsimony analysis and explicitly designed for determining evolutionary relationships among four distantly related taxa. The method is independent of substitution rates because it is derived from consideration of the group properties of substitution operators rather than from an analysis of the probabilities of substitution in branches of a tree. In both parsimony and evolutionary parsimony, three patterns of nucleotide substitution are associated one-to-one with the three topologically linked trees for four taxa. In evolutionary parsimony, the three quantities are operator invariants. These invariants are the remnants of substitutions that have occurred in the interior branch of the tree and are analogous to the substitutions assigned to the central branch by parsimony. The two invariants associated with the incorrect trees must equal zero (statistically), whereas only the correct tree can have a nonzero invariant. The chi 2-test is used to ascertain the nonzero invariant and the statistically favored tree. Examples, obtained using data calculated with evolutionary rates and branchings designed to camouflage the true tree, show that the method accurately predicts the tree, even when substitution rates differ greatly in neighboring peripheral branches (conditions under which parsimony will consistently fail). As the number of substitutions in peripheral branches becomes fewer, the parsimony and the evolutionary-parsimony solutions converge. The method is robust and easy to use.

Base Sequence↗