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PubMed1997

Clonal selection of HIV type 1 variants associated with resistance to foscarnet in vitro: confirmation by molecular evolutionary analysis.

Foscarnet (trisodium phosphonoformate, PFA) is an effective inhibitor of retroviral reverse transcriptase (RT) and is known to block the replication of human immunodeficiency virus type 1 (HIV-1). In this article we analyzed the evolutionary process in generating HIV-1 strains related to drug resistance, using PFA as a selective pressure. PFA inhibited virus replication and protected the virus-induced cell killing, but it did not completely eliminate HIV-1 during the course of 7 weeks of treatment. The nucleotide sequence of the 859-bp DNA fragment spanning the core region of the HIV-1 pol gene was determined for 51 clones obtained from genomic DNA of the HIV-1-infected cells at different time points during PFA treatment. The nucleotide sequence analysis documented the presence of a minor HIV-1 variant prior to the PFA treatment. Molecular evolutionary techniques were utilized to analyze how the minor HIV-1 clones became predominant during this evolutionary process under the selective pressure of PFA. A phylogenetic tree analysis divided these 51 HIV-1 clones into 3 groups. One of the groups consisted of the clones associated with the resistance to PFA. The clones belonging to this group became predominant over time during the course of PFA treatment. Thus, the acquisition of PFA resistance by HIV-1 was considered to be due to clonal selection. Furthermore, among the various amino acid substitutions observed, the substitution of arginine at position 172 by lysine (Arg172Lys) clearly distinguished this group from the others. Since the consistent amino acid substitution observed here has not been identified in the HIV-1 strains resistant to other RT inhibitors, PFA in combination with other RT inhibitors is considered to be a feasible candidate for a convergent combined chemotherapy against HIV-1 in the treatment of patients with AIDS and related conditions.

Amino Acid Sequence↗

PubMed2006

Convergent tapering of xylem conduits in different woody species.

A recent theoretical model (the West, Brown and Enquist, WBE model) hypothesized that plants have evolved a network of xylem conduits with a tapered structure (narrower conduits distally) which should minimize the cost of water transport from roots to leaves. Specific measurements are required to test the model predictions. We sampled both angiosperms and gymnosperms (50 trees) growing in different environments with heights ranging from 0.5 to 44.4 m, measuring variations of the xylem-conduit diameter from tree top to stem base. In all trees measured, mean hydraulically weighted conduit diameters (Dh) at the tree top were narrower than those at the stem base. In actively growing trees, the longitudinal variation of Dh showed a degree of tapering in agreement with WBE predictions, while trees close to their maximum height showed slightly lower conduit tapering. Comparing different species, a very good correlation was observed between degree of xylem tapering and tree height (r2 = 0.88; P < 0.0001) independently of any other variable (age, site, altitude, etc.). As predicted by WBE, sampled trees seemed to converge towards similar xylem conduit tapering. However, trees approaching their maximum height had a nonoptimal tapering which appeared insufficient to compensate for the progressive increase in tree height.

Biological Evolution↗

PubMed2004

A new model for olfactory placode development.

The peripheral nervous system of vertebrate animals arises primarily from the interaction of cranial neural crest and sensory placodes. Placodes are described as thickenings of ectoderm that arise through cell division during neural tube formation. The olfactory sensory system is one component of the peripheral nervous system that arises from paired sensory placodes during development. The olfactory placodes give rise to the primary sensory neurons, support cells and basal cells of the olfactory epithelium. Recent evidence from work in zebrafish and chick suggests that the olfactory and auditory placodes arise from large fields of cells that converge to form the sensory placode. The olfactory placodes arise from within the neural plate, and cell division is apparent only after the sensory placodes are morphologically distinct. As the olfactory placode is forming, its precursors must segregate from their neighboring fields which will give rise to the adenohypophyseal placode, cranial neural crest, and telencephalon. Analysis has shown that the endocrine cells thought to arise from the olfactory placode originate in the neighboring adenohypophyseal and cranial neural crest domains. The borders separating the domains are plastic, where cells sort as they move, and cell fate is dependent on the identity of neighbors once the cells have converged to form the sensory placode. Thus there is degeneracy built into the system such that cells accommodate changes in the environment until cell migrations controlling the formation of the sensory placodes are complete.

Animals↗

PubMed2000

Genetic algorithm for ellipsometric data inversion of absorbing layers.

A new data reduction method is presented for single-wavelength ellipsometry. A genetic algorithm is applied to ellipsometric data to find the best fit. The sample consists of a single absorbing layer on a semi-infinite substrate. The genetic algorithm has good convergence and is applicable to many different problems, including those with different independent measurements and situations with more than two angles of incidence. Results are similar to those obtained by other inversion techniques.

Algorithms↗

PubMed1975

Models for cultural inheritance: a general linear model.

A theory of cultural evolution is proposed based on a general linear mode of cultural transmission. The trait of an individual is assumed to depend on the values of the same trait in other individuals of the same, the previous or earlier generation. The transmission matrix W has as its elements the proportional contributions of each individual (i) of one generation to each individual (j) of another. In addition, there is random variation (copy error or innovation) for each individual. Means and variances of a group of N individuals change with time and will stabilize asymptotically if the matrix W is irreducible and aperiodic. The rate of convergence is geometric and is governed by the largest non-unit eigenvalue of W. Groups fragment and evolve independently if W is reducible. The means of independent groups vary at random at a predicted rate, a phenomenon termed "random cultural drift". Variances within a group tend to be small, assuming cultural homogeneity. Transmission matrices of the teacher/leader type, and of parental type have been specifically considered, as well as social hierarchies. Various limitations, extensions, and some chances of application are discussed.

Cultural Evolution↗

PubMed1991

[Evolution and demographic characteristics of native groups in Canada, 1986-2011].

Population estimates and projections are presented and analyzed for the period 1986-2011 for the Native American population living in Canada. The analysis considers census underenumeration and the impact of recent legislation that increased the number of residents with Native American status by approximately 25 percent. It is concluded that "native groups will continue to grow at a higher rate than the Canadian population as a whole. Comparing the two populations shows a convergence for some demographic characteristics; however, the aging of the native population started much later." (SUMMARY IN ENG AND SPA)

Americas↗

PubMed2000

Molecular phylogenetics of the holly leafminers (Diptera: Agromyzidae: Phytomyza): species limits, speciation, and dietary specialization.

A molecular phylogenetic analysis was conducted to determine relationships and to investigate character evolution in the Phytomyza ilicis group of leafmining flies on hollies (Aquifoliaceae: Ilex). A total of 2207 bp of the mitochondrial cytochrome oxidase I and II genes were sequenced for all known holly leafminers, as well as for several undescribed members of this group. Maximum-parsimony analysis of the sequence data indicates that these leafminers form a monophyletic group with the inclusion of an undescribed leafminer that feeds on the distantly related plant Gelsemium sempevirens (Loganiaceae). Species boundaries of previously known and of undescribed holly leafmining species were confirmed with the molecular data, with one exception. Optimization of variable ecological and morphological characters onto the most parsimonious phylogeny suggests that these traits are evolutionarily labile, requiring multiple instances of convergence and/or reversal to explain their evolutionary history. Speciation in holly leafminers is associated with host shifts and appears to involve colonization of new hosts more often than cospeciation as the hosts diverge. Monophagy is the most common feeding pattern in holly leafminers, and more generalized feeding is inferred to have evolved at least two separate times, possibly as a prelude to speciation.

Animals↗

PubMed1998

Updated measurements from CREAM & CREDO & implications for environment & shielding models.

Flight data obtained between 1995 and 1997 from the Cosmic Radiation Environment Monitors CREAM & CREDO carried on UoSat-3, Space Shuttle, STRV-1a (Space Technology Research Vehicle) and APEX (Advanced Photovoltaic and Electronics Experiment Spacecraft) have been added to the dataset affording coverage since 1990. The modulation of cosmic rays and evolution of the South Atlantic Anomaly are observed, the former comprising a factor three increase at high latitudes and the latter a general increase accompanied by a westward drift. Comparison of particle fluxes and linear energy transfer spectra is made with improved environment & radiation transport calculations which account for shield distributions and secondary particles. While there is an encouraging convergence between predictions and observations, significant improvements are still required, particularly in the treatrnent of locally produced secondary particles.

Atlantic Ocean↗

PubMed1983

Do retinal and spinal projections overlap within the turtle thalamus?

The spinal and retinal projections to the turtle thalamus were studied using the autoradiographic tracing technique. Particular attention is given to the regions receiving both spinal and retinal projections: the ovalis complex and a perirotundal stripe. Spinal and retinal projections do not overlap significantly in either of these regions. In the perirotundal stripe there appears to be little likelihood of convergence of these projections on single neurons. In the ovalis complex, the most densely and the most consistently innervated thalamic region, however, the respective spinal and retinal target areas are located immediately adjacent to each other and low order somatosensory and visual projections may converge on single neurons with dendrites extending into both the spinal and retinal terminal arborizations. The ovalis complex in the turtle may be compared with the ventral part of the mammalian lateral geniculate nucleus. Both these nuclei receive spinal and retinal projections and both, reportedly, do not project to the telencephalon. The findings are discussed in relation to the possible evolution of the specific thalamic sensory nuclei in higher mammals as well as to the prosencephalic processing of somatosensory and visual information in turtles and mammals.

Animals↗

PubMed1990

Nash equilibrium and evolutionary stability in large- and finite-population "playing the field" models.

This paper studies the correspondence between Nash equilibrium and evolutionary stability in large- and finite-population "playing the field" models. Whenever the fitness function is sufficiently continuous, any large-population ESS corresponds to a symmetric Nash equilibrium in the game that describes the simultaneous interaction of the individuals in the population, and any strict, symmetric Nash equilibrium in that game corresponds to a large-population ESS. This correspondence continues to hold, approximately, in finite populations; and it holds exactly for strict pure-strategy equilibria in sufficiently large finite populations. By contrast, a sequence of (mixed-strategy) finite-population ESSs can converge, as the population grows, to a limit that is not a large-population ESS, and a large-population ESS need not be the limit of any sequence of finite-population ESSs.

Animals↗

PubMed2006

Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus.

The introduction of plastids into different heterotrophic protists created lineages of algae that diversified explosively, proliferated in marine and freshwater environments, and radically altered the biosphere. The origins of these secondary plastids are usually inferred from the presence of additional plastid membranes. However, two examples provide unique snapshots of secondary-endosymbiosis-in-action, because they retain a vestige of the endosymbiont nucleus known as the nucleomorph. These are chlorarachniophytes and cryptomonads, which acquired their plastids from a green and red alga respectively. To allow comparisons between them, we have sequenced the nucleomorph genome from the chlorarachniophyte Bigelowiella natans: at a mere 373,000 bp and with only 331 genes, the smallest nuclear genome known and a model for extreme reduction. The genome is eukaryotic in nature, with three linear chromosomes containing densely packed genes with numerous overlaps. The genome is replete with 852 introns, but these are the smallest introns known, being only 18, 19, 20, or 21 nt in length. These pygmy introns are shown to be miniaturized versions of normal-sized introns present in the endosymbiont at the time of capture. Seventeen nucleomorph genes encode proteins that function in the plastid. The other nucleomorph genes are housekeeping entities, presumably underpinning maintenance and expression of these plastid proteins. Chlorarachniophyte plastids are thus serviced by three different genomes (plastid, nucleomorph, and host nucleus) requiring remarkable coordination and targeting. Although originating by two independent endosymbioses, chlorarachniophyte and cryptomonad nucleomorph genomes have converged upon remarkably similar architectures but differ in many molecular details that reflect two distinct trajectories to hypercompaction and reduction.

Base Sequence↗

PubMed2005

Maximum likelihood Jukes-Cantor triplets: analytic solutions.

Maximum likelihood (ML) is a popular method for inferring a phylogenetic tree of the evolutionary relationship of a set of taxa, from observed homologous aligned genetic sequences of the taxa. Generally, the computation of the ML tree is based on numerical methods, which in a few cases, are known to converge to a local maximum on a tree, which is suboptimal. The extent of this problem is unknown, one approach is to attempt to derive algebraic equations for the likelihood equation and find the maximum points analytically. This approach has so far only been successful in the very simplest cases, of three or four taxa under the Neyman model of evolution of two-state characters. In this paper we extend this approach, for the first time, to four-state characters, the Jukes-Cantor model under a molecular clock, on a tree T on three taxa, a rooted triple. We employ spectral methods (Hadamard conjugation) to express the likelihood function parameterized by the path-length spectrum. Taking partial derivatives, we derive a set of polynomial equations whose simultaneous solution contains all critical points of the likelihood function. Using tools of algebraic geometry (the resultant of two polynomials) in the computer algebra packages (Maple), we are able to find all turning points analytically. We then employ this method on real sequence data and obtain realistic results on the primate-rodents divergence time.

Biological Evolution↗

PubMed2005

Courting bird sings with stridulating wing feathers.

In birds and other vertebrates, most acoustic signals are produced pneumatically by moving air through a vocal apparatus. Here we describe a unique mechanism used to produce a tonal acoustic signal in vertebrates. Video recordings of the courtship displays of male Club-winged Manakins, Machaeropterus deliciosus, reveal that males produce sustained harmonic tones through interactions among oscillating secondary wing feathers. This mechanism of sound production shows morphological and mechanistic convergence with arthropod stridulation. Intersexual selection for production of a nonvocal courtship song has led to major morphological, functional, and likely physiological modifications in the wing of this flying bird.

Animal Communication↗

PubMed2005

Chitin induces natural competence in Vibrio cholerae.

The mosaic-structured Vibrio cholerae genome points to the importance of horizontal gene transfer (HGT) in the evolution of this human pathogen. We showed that V. cholerae can acquire new genetic material by natural transformation during growth on chitin, a biopolymer that is abundant in aquatic habitats (e.g., from crustacean exoskeletons), where it lives as an autochthonous microbe. Transformation competence was found to require a type IV pilus assembly complex, a putative DNA binding protein, and three convergent regulatory cascades, which are activated by chitin, increasing cell density, and nutrient limitation, a decline in growth rate, or stress.

Animals↗

PubMed2001

Neural network control systems that learn to perform appropriately.

Setting up a neural network with a learning algorithm that determines how it can best operate is an efficient way to formulate control systems for many engineering applications, and is often much more feasible than direct programming. This paper examines three important aspects of this approach: the details of the cost function that is used with the gradient descent learning algorithm, how the resulting system depends on the initial pre-learning connection weights, and how the resulting system depends on the pattern of learning rates chosen for the different components of the system. We explore these issues by explicit simulations of a toy model that is a simplified abstraction of part of the human oculomotor control system. This allows us to compare our system with that produced by human evolution and development. We can then go on to consider how we might improve on the human system and apply what we have learnt to control systems that have no human analogue.

Computer Simulation↗

PubMed1996

The beta-ketoadipate pathway and the biology of self-identity.

The beta-ketoadipate pathway is a chromosomally encoded convergent pathway for aromatic compound degradation that is widely distributed in soil bacteria and fungi. One branch converts protocatechuate, derived from phenolic compounds including p-cresol, 4-hydroxybenzoate and numerous lignin monomers, to beta-ketoadipate. The other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates. Enzyme studies and amino acid sequence data indicate that the pathway is highly conserved in diverse bacteria, including Pseudomonas putida, Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Rhodococcus erythropolis, and many others. The catechol branch of the beta-ketoadipate pathway appears to be the evolutionary precursor for portions of the plasmid-borne ortho-pathways for chlorocatechol degradation. However, accumulating evidence points to an independent and convergent evolutionary origin for the eukaryotic beta-ketoadipate pathway. In the face of enzyme conservation, the beta-ketoadipate pathway exhibits many permutations in different bacterial groups with respect to enzyme distribution (isozymes, points of branch convergence), regulation (inducing metabolites, regulatory proteins), and gene organization. Diversity is also evident in the behavioral responses of different bacteria to beta-ketoadipate pathway-associated aromatic compounds. The presence and versatility of transport systems encoded by beta-ketoadipate pathway regulons is just beginning to be explored in various microbial groups. It appears that in the course of evolution, natural selection has caused the beta-ketoadipate pathway to assume a characteristic set of features or identity in different bacteria. Presumably such identities have been shaped to optimally serve the diverse lifestyles of bacteria.

Adipates↗

PubMed2001

Fibrinogen stimulates macrophage chemokine secretion through toll-like receptor 4.

Extravascular fibrin deposition is an early and persistent hallmark of inflammatory responses. Fibrin is generated from plasma-derived fibrinogen, which escapes the vasculature in response to endothelial cell retraction at sites of inflammation. Our ongoing efforts to define the physiologic functions of extravasated fibrin(ogen) have led to the discovery, reported here, that fibrinogen stimulates macrophage chemokine secretion. Differential mRNA expression analysis and RNase protection assays revealed that macrophage inflammatory protein-1alpha (MIP-1alpha), MIP-1beta, MIP-2, and monocyte chemoattractant protein-1 are fibrinogen inducible in the RAW264.7 mouse macrophage-like cell line, and ELISA confirmed that both RAW264.7 cells and primary murine thioglycolate-elicited peritoneal macrophages up-regulate the secretion of monocyte chemoattractant protein-1 >100-fold upon exposure to fibrinogen. Human U937 and THP-1 precursor-1 (THP-1) monocytic cell lines also secreted chemokines in response to fibrinogen, upon activation with IFN-gamma and differentiation with vitamin D(3), respectively. LPS contamination could not account for our observations, as fibrinogen-induced chemokine secretion was sensitive to heat denaturation and was unaffected by the pharmacologic LPS antagonist polymyxin B. Nevertheless, fibrinogen- and LPS-induced chemokine secretion both apparently required expression of functional Toll-like receptor 4, as each was diminished in macrophages derived from C3H/HeJ mice. Thus, innate responses to fibrinogen and bacterial endotoxin may converge at the evolutionarily conserved Toll-like recognition molecules. Our data suggest that extravascular fibrin(ogen) induces macrophage chemokine expression, thereby promoting immune surveillance at sites of inflammation.

Animals↗

PubMed2001

[Oocyst structure and problem of coccidian taxonomy].

A comparative ultrastructural study was made of both thin- and thick-walled oocysts of Cryptosporidium parvum. According to the authors' findings, all the oocysts in C. parvum should be considered as thin-walled, since their walls have been composed of a single membrane or of two, closely apposed membranes without any additional substance in between. Despite the presence of two types of wall-forming bodies (WFB) in the maturing macrogamete or zygote, there is no evidence of their involvement in oocyst wall formation. In this concern, the function and destiny of WFB in C. parvum oocysts still remain obscure. Similar structure of the oocysts wall was reported elsewhere for thin-walled oocysts of fish coccidia of the genera Goussia and Eimeria. In C. parvum, the "thick-walled" oocysts differ from oocysts with thin walls in the availability in the former of a single sporocyst. The sporocyst wall consists of two unequal layers: a thin outer layer and a thicker inner one, in which a characteristic suture line is occasionally seen. By this feature the thick-walled oocysts of C. parvum bear similarities with oocysts of the cyst-forming coccidia (Cystoisospora, Toxoplasma, Sarcocystis) and of the genus Goussia: in all these the valves making up the sporocyst wall are joint just along the suture line. The literary and the authors' own data make it possible to suppose that the suture detected in C. parvum oocysts is located in the sporocyst wall, joining its valves, rather than in the oocyst wall proper, known to be composed of one or two, closely apposed unit membranes. Again, the availability of a suture (or sutures) in the sporocyst hardly provides enough reason to relate C. parvum with either cyst-forming, or fish coccidia, since this structure itself may be of a convergency character, rather than of systematic value. This may be substantiated, at least in part, by the authors' previous findings (Beyer, Sidorenko, 1984) of a similar structure, originally referred to as a "slit channel", in the intraerythrocytic capsule around gamont stage of haemogregarines--the adeleid coccidia of the genus Karyolysus. The suture-like structure could have originated in the evolution independently in different groups of parasitic protozoa to serve eventually as a suitable mechanism for immediate separation of elements involved in protective formation harbouring different developmental stages, including, for example, sporozoites in the eimeriid coccidia, or gamonts in the adeleid coccidia.

Animals↗