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PubMed2026

Exploring the Effect of Whole-Genome Duplication on Salmonid LincRNA Repertoire.

Long intergenic non-coding RNAs (lincRNAs) are key epigenetic regulators of genome function, yet their evolutionary dynamics following whole-genome duplication (WGD) events remain poorly understood. Salmonids, which underwent a lineage-specific autotetraploidization (salmonid-specific WGD, ~88-100 million years ago), provide an excellent model to investigate the retention, divergence, and functional potential of recently duplicated non-coding elements. LincRNA repertoires were compared across five genome-annotated salmonids (Oncorhynchus tshawytscha, O. kisutch, O. mykiss, Salmo salar, and S. trutta) and their closest non-duplicated relative, northern pike (Esox lucius). LincRNAs represented ~5-7% of annotated genes in all salmonids except S. salar (18%). Sequence conservation was low relative to coding genes, with only 11-68 highly similar (e-value < 1 × 10-30; similarity > 70% and alignments > 100 nucleotides) putative orthologues shared between salmonids and northern pike, and 161-338 among salmonids alone. Synteny conservation was modest in lincRNAs, with lower conservation in putative orthologues (8-16%) compared to putative ohnologues (8-33%). Secondary structure conservation was associated with sequence similarity (ρ = -0.45; p = 2.2 × 10-16), and the association was stronger among WGD ohnologues than orthologues. In S. salar and O. mykiss, lincRNA putative ohnologues showed weaker expression correlations than coding genes, suggesting widespread regulatory divergence, possibly through neo- and subfunctionalisation. Conserved salmonid lincRNAs showed enriched predicted interactions with miRNAs involved in tumour suppression, brain, bone, and muscle development (e.g., miR-455, miR-365, miR124, miR-133a, miR-140, and miR-9), a finding supported by limited transcriptomic data. Although salmonid WGD expanded lincRNA repertoires, lincRNAs have undergone rapid sequence and transcriptional divergence, with limited conservation across species based on sequence similarity, chromosomal position, synteny, and secondary structure. A subset of conserved lincRNAs retains structural features and regulatory signatures consistent with roles as miRNA sponges in brain, skeletal, and muscle development and tumour suppression, potentially acting within conserved regulatory networks. These findings provide new insights into lincRNA evolution following genome duplication and highlight the need for experimental validation of their regulatory functions.

Animals↗

PubMed2006

Controlled synthesis of high-quality PbS star-shaped dendrites, multipods, truncated nanocubes, and nanocubes and their shape evolution process.

Well-defined single-crystalline PbS nano- and microstructures including dendrites, multipods, truncated nanocubes, and nanocubes were synthesized in high yield by a simple solution route. Novel star-shaped PbS dendrites with six symmetric arms along the 100 direction, each of which shows one trunk (long axis) and four branches (short axes), have been achieved using Pb(AC)2 and thioacetamide (TAA) as precursors, under the molar ratio Pb(AC)2/TAA = 2/1, at initial reaction temperature 80 degrees C, refluxing for 30 min at 100 degrees C, in the presence of cetyltrimethylammonium bromine (CTAB). The "nanorods" in each branch are parallel to each other in the same plane and are perpendicular to the trunk. The truncated nanocubes mainly bounded by the {100} plane were prepared under a different Pb(AC)2/TAA molar ratio, at initial reaction temperature 40 degrees C, refluxing for 12 h at 100 degrees C. Based on the systematic studies on their shape evolution, a possible growth mechanism of these PbS nano- and microstructures was proposed. The shapes of PbS nanocrystals with face-centered cubic (fcc) structure are mainly determined by the ratio (R) between the growth rates along the (100) and (111) directions. The Pb(AC)2/TAA molar ratio and the initial reaction temperature influence the growth ratio R in the formation of PbS nuclei at an early stage, which results in the final morphology of PbS nanocrystals. Under the current experimental conditions, we can control the PbS shape evolution by simply tuning the molar ratio, the initial reaction temperature, and the period of reaction. Based on the systematic studies on the shape evolution, this approach is expected to be employed for the control-shaped synthesis of other fcc structural semiconductor nanomaterials. The photoluminescence properties were investigated and the prepared nano- and microstructures displayed a very strong luminescence around 600-650 nm at room temperature.

Journal Article↗

PubMed1999

Helping behaviour in facultatively eusocial hover wasps: an experimental test of the subfertility hypothesis.

A candidate explanation for the evolution of eusociality is that helpers are physiologically constrained such that helping is their only realistic option. We tested this subfertility hypothesis in a species of facultatively eusocial hover wasp (Hymenoptera, Stenogastrinae: Liostenogaster flavolineata) by seeing whether helpers that were forced to nest on their own were able to mature their own eggs. One focal helper was left alone on each of 22 nests, from which all other adult wasps (including the dominant) were permanently removed. After 18 days, all but one of the 19 focal helpers that remained on their nests had ovarian development and insemination status characteristic of dominants, and the majority had probably laid eggs. This was in striking contrast to the reproductive status of other helpers removed from the same nests at the start of the experiment. These results provide convincing experimental evidence that females do not become helpers because of some unconditional physiological constraint. There is currently no unequivocal support for the subfertility hypothesis in facultatively eusocial Hymenoptera lacking morphological castes. Copyright 1999 The Association for the Study of Animal Behaviour.

Journal Article↗

PubMed2005

Modeling for radio-frequency conductive keratoplasty: implications for the maximum temperature reached in the cornea.

Conductive keratoplasty (CK) is a new surgical technique for steepening the contours of the cornea to reduce hyperopia. It has been emphasized that during CK, tissue resistance to radio-frequency electrical current flow generates a localized heat with temperatures between 65 and 75 degrees C; however, we hypothesize that the maximum temperature reached in the cornea may be higher. For this reason, we developed a finite-element model to estimate the temperature distributions in the cornea during CK. The time evolution of the impedance obtained from computer simulations was compared to that obtained in an experimental study previously published. Our results show that during a typical CK with a 60% setting power (equivalent to 200 V peak-to-peak), the cornea may reach temperatures over 100 degrees C at the electrode tip. On the other hand, the initial impedance of the cornea has a significant influence on the temperature distribution, while the initial temperature of the cornea is not a significant parameter. The results also suggest that low power settings (30-40%) do not produce temperatures over 100 degrees C. Finally, although the actual voltage waveform during CK is exponential and pulsed, our model based on a constant voltage (with a value equal to the root mean square value) provides a better agreement between the theoretical impedance time evolution and that obtained experimentally.

Animals↗

PubMed2002

Magnetization evolution in network models of porous rock under conditions of drainage and imbibition.

Surface-enhanced relaxation of nuclear magnetization in fully and partially saturated water-wet porous media is studied using a pore network simulator. The simulator is based on a description of the pore space in terms of a regular cubic lattice of pores and throats following respective size distributions. The latter are obtained from geometric characterization of 3D stochastic replicas of real porous rock samples. Concepts of percolation theory are used to simulate the pore-scale distribution of a strongly wetting phase under conditions of quasistatic drainage by or imbibition against a nonwetting phase. The results of these simulations compare favorably with experimental mercury intrusion/retraction curves. The equations governing magnetization evolution in a connected pore system are then solved by matrix diagonalization for different values of wetting-phase saturation along the primary drainage and secondary imbibition paths. Analysis of the corresponding spectra of decay rates provides new insights regarding the influence of pore structure (pore and throat size distributions, spatial correlation), surface relaxation strength, and fluid distribution on diffusive coupling between pores. For pore and throat size distributions and surface relaxation strength representative of sandstones, diffusive coupling is quite important, especially under conditions of partial saturation. Remarkably, simulations show that correlated heterogeneity is the main reason pores appear poorly coupled with respect to NMR relaxation-an assumption underlying the correspondence between pore size and relaxation time distributions. Finally, for a given value of wetting-phase saturation, the history of saturation change (drainage or imbibition) is shown to have a profound effect on the spectrum of decay rates.

Journal Article↗

PubMed1991

Evolution in molecular structure and adaptive variance in metabolism.

1. A hypothesis is advanced to the effect that all metabolites, even minor ones, are expressed as a result of stimuli and are directed against or support actions on receptor systems. 2. In particular the hypothesis emphasizes the dynamic character of the secondary metabolite pattern as a function of physiological or environmental conditions and that the variations observed reflect the evolution of receptors. 3. Predictions based on this principle are experimentally verifiable. 4. The hypothesis has major implications in the entire area of life sciences.

Biological Evolution↗

PubMed1981

Proliferation of preneoplastic lesions after discontinuation of chronic DEN feeding in the development of hepatomas in rat.

Diethylnitrosamine (DEN, 10 mg/kg/day) was fed to rats for 2, 4 and 6 weeks. At different times after feeding with DEN was stopped, growth of preneoplastic lesions has been correlated with pathological evolution (preneoplastic foci, neoplastic nodules and hepatomas). The proliferating fraction in the foci, the cell content, and relative volume of foci increase as a function of the duration of the treatment. The proliferating fraction increases evenly throughout the liver, but, in all experimental modalities, preneoplastic cells show a proliferative advantage over the phenotypically normal tissue. In each experimental group, the proliferative rate correlates with the pathological evolution. After 2 weeks of DEN feeding the growth activity of foci remains very low, and neoplastic nodules are not detectable until the median time of death (14 months). After 4 and 6 weeks, a critical size of the foci is reached, corresponding to the neoplastic transformation, and an increased labelling index is triggered in the lesions and in the phenotypically normal tissue. It is speculated that the "growth pressure" induced by the first carcinogen treatment, associated with the subsequent disturbance of the mitotic control regulation, may be implicated in the process of malignant transformation of preneoplastic lesions.

Animals↗

PubMedDate not supplied

What have two decades of laboratory life-history evolution studies on Drosophila melanogaster taught us?

A series of laboratory selection experiments on Drosophila melanogaster over the past two decades has provided insights into the specifics of life-history tradeoffs in the species and greatly refined our understanding of how ecology and genetics interact in life-history evolution. Much of what has been learnt from these studies about the subtlety of the microevolutionary process also has significant implications for experimental design and inference in organismal biology beyond life-history evolution, as well as for studies of evolution in the wild. Here we review work on the ecology and evolution of life-histories in laboratory populations of D. melanogaster, emphasizing how environmental effects on life-history-related traits can influence evolutionary change. We discuss life-history tradeoffs - many unexpected - revealed by selection experiments, and also highlight recent work that underscores the importance to life-history evolution of cross-generation and cross-life-stage effects and interactions, sexual antagonism and sexual dimorphism, population dynamics, and the possible role of biological clocks in timing life-history events. Finally, we discuss some of the limitations of typical selection experiments, and how these limitations might be transcended in the future by a combination of more elaborate and realistic selection experiments, developmental evolutionary biology, and the emerging discipline of phenomics.

Adaptation, Physiological↗

PubMed2002

Effect of hydrolysis on the phase evolution of water-based sol-gel hydroxyapatite and its application to bioactive coatings.

In a previous report, we demonstrated a successful synthesis of crystalline hydroxyapatite (HA) through the use of a water-based sol-gel process. It was shown that the apatite can be obtained at temperatures generally below 400 degrees C, providing a great advantage for practical bioactive coating purposes. The influence of hydrolysis of phosphorus sol solution on the phase evolution of the resulting HA is the focus of this investigation. Experimental results show that, in the absence of acid catalyst, a long-term hydrolysis, i.e. >4 h, is required for better evolution of apatitic phase. Such a phase evolution is mainly attributed to an increased concentration of apatitic phase, rather than improved crystallinity in the calcined gels. With the aid of acid catalyst, we found that a well-crystalline HA can be synthesized over a time period shorter by 2-3 orders of magnitude than those without catalyst, i.e. a few minutes. In almost all cases, a small amount of tricalcium phosphate (TCP) was detected, which may be explainable by the formation of oligomeric derivatives of the phosphorus sol during synthesis, where calcium phosphate derivatives with lower Ca/P ratio than stoichiometry can be developed. By selecting an optimal sol as a dipping source, highly-porous dental root specimens were coated and a thin, dense, adhesive (upon finger-nail scratching test) coating was achieved after calcinations at 375 degrees C. An in vitro test also shows a bioactive character of the coating.

Journal Article↗

PubMed2005

Reproductive compensation in the evolution of plant mating systems.

Reproductive compensation, the replacement of dead embryos by potentially viable ones, is known to play a major role in the maintenance of deleterious mutations in mammalian populations. However, it has received little attention in plant evolution. Here we model the joint evolution of mating system and inbreeding depression with reproductive compensation. We used a dynamic model of inbreeding depression, allowing for partial purging of recessive lethal mutations by selfing. We showed that reproductive compensation tended to increase the mean number of lethals in a population, but favored self-fertilization by effectively decreasing early inbreeding depression. When compensation depended on the selfing rate, stable mixed mating systems can occur, with low to intermediate selfing rates. Experimental evidence of reproductive compensation is required to confirm its potential importance in the evolution of plant mating systems. We suggest experimental methods to detect reproductive compensation.

Biological Evolution↗

PubMed1997

Three dimensional imaging of the Belousov-Zhabotinsky reaction using magnetic resonance.

The combination of 3D magnetic resonance imaging data with polygon based computer graphic display software is ideally suited to the study of the Belousov-Zhabotinsky reaction in extended volumes. In this paper we present the first true three dimensional visualization of experimental data from the Belousov-Zhabotinsky reaction. The time evolution of a twisted scroll wave like isoconcentration surface and its organizing filament are demonstrated for the manganese-catalyzed B-Z mixture. These techniques extend the experimental study of the B-Z reaction as a class of pattern-forming systems to the third dimension. The limitations of the technique are discussed.

Computer Simulation↗

PubMed2005

An evolutionary relationship between genetic variation and phenotypic fluctuation.

The relevance of phenotype fluctuations among clones (i.e., organisms with identical genes) to evolution has recently been recognized both theoretically and experimentally. By considering the stability of the distributions of genetic variations and phenotype fluctuations, we derive a general inequality between the phenotype variance due to genetic differences and the intrinsic phenotype variance of clones. For a given mutation rate, an approximately linear relationship between the two is obtained which elucidates the consistency between the fundamental theorem of natural selection by Fisher and the evolutionary fluctuation-response relationship (fluctuation dissipation theorem) proposed recently. A general condition for the error catastrophe is also derived as the violation of the inequality, which sets up the limit to the speed of stable evolution. All of these theoretical results are confirmed by a numerical evolution experiment of a cell that consists of a catalytic reaction network. Based on the relationships proposed here, relevance of the phenotypic plasticity to evolution as well as the genetic assimilation is discussed.

Animals↗

PubMed2001

The outlook for cosmic company.

The last 100 million years or so has seen a continued increase in encephalization for several terrestrial species. Intelligence has survival value. Developments in astrobiology suggest that what was once considered enormously improbable, namely life, is now suspected of being ubiquitous. It may be that the evolution of intelligence is unlikely, but in a finite, breathtakingly large universe (10(22) stars) small probability likely does not matter. Even if nature is indifferent to producing intelligence, SETI might still succeed. Biological intelligence may be rare, but it has the potential for creating engineered synthetic intelligence, capable of rapid and directed self-evolution. The galaxy could be rife with such long-lived, communicating devices, even if intelligent protoplasm is both rare and fleeting. SETI is looking for narrow-band, microwave signals that are not produced naturally. Ultimately, SETI is more exploration than experimentation.

Artificial Intelligence↗

PubMed2005

Plasma ion evolution in the wake of a high-intensity ultrashort laser pulse.

Experimental investigations of the late-time ion structures formed in the wake of an ultrashort, intense laser pulse propagating in a tenuous plasma have been performed using the proton imaging technique. The pattern found in the wake of the laser pulse shows unexpectedly regular modulations inside a long, finite width channel. On the basis of extensive particle in cell simulations of the plasma evolution in the wake of the pulse, we interpret this pattern as due to ion modulations developed during a two-stream instability excited by the return electric current generated by the wakefield.

Journal Article↗

PubMed1999

Experimental and numerical study of pulsatile flows through stenosis: wall shear stress analysis.

Different shapes of pulsatile flows through a model of stenosis are experimentally and numerically modeled to validate both methods and to determine the wall shear stress temporal evolution downstream from the stenosis. Two-dimensional velocity measurements are performed in a 75% severity stenosis using a pulsed Doppler ultrasonic velocimeter. Finite element package is employed for the transient numerical simulations. Polynomial method, based on the experimental velocity values, is proposed to determine the wall shear stress temporal evolution. There is a good agreement between the numerical and experimental results. The wall shear stress temporal analysis shows oscillating wall shear stress values during the cycle with high wall shear stress values at the throat of about 120 dyn/cm2, and low values downstream from the stenosis of about - 2.5 dyn/cm2. The key result of the study is that the presence of the stenosis leads the artery to work in a direction which is opposite to the direction of a healthy artery.

Animals↗

PubMed1994

An approach to the in vitro study of the UTP/UDPglucose/UDP moiety-conserved cycle.

The kinetic behavior of a moiety-conserved ternary cycle is tested experimentally. This system contains the enzymes UDPglucose pyrophosphorylase, glycogen synthase and nucleoside diphosphokinase, converting respectively UTP into UDPglucose, then into UDP and back to UTP in a cyclic manner. The UDPGlc P2ase and NDPK steps are made irreversible by addition of inorganic pyrophosphatase and phosphocreatine kinase, respectively. In order to predict both the evolution and the steady-state values of the various substrates, a model is derived, which takes into account the actual enzyme rate expressions and parameter values, as determined under our experimental conditions. In that model, the UTP, UDPglucose and UDP are taken as the variables, whereas the total concentration of the substrate pool and the four enzyme maximal activities are chosen as the control parameters. Depending upon the various parameter values, monostability, reversible bistability and irreversible transitions may theoretically occur. However, it turns out that some of these values for which multistability might occur, are not accessible experimentally. Under conditions of monostability, the evolutions of the three substrates as experimentally measured are shown to be in good qualitative and quantitative agreement with the model predictions. The relaxation times between two consecutive steady states when a parameter is varied, are shown to be long-lasting processes (several hours). That such an experimental ternary substrate cycle actually exhibits a low sensitivity to any perturbation, addresses the issue to knowing if the same property is likely to occur in vivo, or, in other words, do large moiety-conserved cycles act as metabolic buffers?

Animals↗

PubMed1983

The role of the institutional review board in research involving human subjects.

Concern with the rights and welfare of human experimental research subjects has given rise to the evolution of institutional review boards. This article describes the basic composition and purposes of these boards, as well as the federal regulations by which they are governed. Since many of these regulations are open to interpretation, the policies and procedures of one such board are included to represent an example of how these regulations are interpreted and applied.

Documentation↗

PubMed2002

The behavior and the morphology of sea lilies with shortened stalks: implications on the evolution of feather stars.

Extant crinoids can be divided into two groups, stalked sea lilies and stalkless feather stars. Feather stars are considered to have evolved from stalked ancestors by losing most of the stalk, but other differences are present between the two groups. The unsegmented centrodorsal, long and curved cirri near the crown, small calyx, and the ability to swim are all feather star features not found in the sea lilies. To figure out which of the above features evolved directly correlating with loss of the stalk in feather stars, we cut off the stalk from the sea lily Metacrinus rotundus and kept them alive in an aquarium. The specimens with shortened stalks were able to stand and crawl with their arms without the support of their stalks, but swimming was not observed for any of the animals. Morphologically, neither fusion of the remaining segments nor the reduction of the size of the calyx were observed, but the cirri became long and curved near the crown. Therefore, the extant sea lilies possess a potential to adapt to incidents of stalk loss. Specimens autotomizing most of their stalks were observed, suggesting that the potential is actually employed in nature. This mechanism linking the reduction of the stalk and the changes in the morphology of cirri may have played an important role in the evolution of the feather stars, if the stalked ancestors of feather stars also possessed this potential. Experimental zoological approaches as this study may provide new insights to the questions of evolution.

Animals↗