SEARCH · PubMed Health

Results for “Extinction, Biological”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,243 records · Page 69Linked to original sources

PubMed1993

Photosensitization with bacteriochlorins.

Biophysical and photobiological properties of a group of bacteriochlorins were compared with efficacy of these products for photodynamic therapy of murine tumors. Predictive factors for selective photosensitization in vivo include affinity binding to lipoproteins greater than albumin, extinction coefficient at the wavelength of irradiation and tumor/skin distribution. Efficacy was correlated with circulating plasma levels of the different sensitizers but not with the photodynamic therapy response in cell culture.

Animals↗

PubMedDate not supplied

Relevance of in vitro studies for in vivo aging.

Cell cultures have allowed some fundamental mechanisms of cellular biology relevant to the aging process to be studied. The deregulation of events such as cell migration, response to growth stimuli, and inductive interactions between different cell systems have been analyzed and some of the underlying molecular mechanisms were identified. A genome reorganization taking place in the hierarchical structures of DNA during cellular aging could be ascertained. The remodeling occurring in organs, tissues, and cells during aging can be now seen as the result of the structural reorganization observed at the molecular level that progresses continuously from fertilization of the egg to the extinction of the organism. This remodeling occurs in such a way as to decrease the capacity for subsequent change, approaching a condition of equilibrium; aging can be seen as the tendency to reach this limit.

Animals↗

PubMed1983

Yeast tRNAAsp-aspartyl-tRNA synthetase: the crystalline complex.

Aspartyl-tRNA synthetase from yeast, a dimer of molecular weight 125,000 and its cognate tRNA (Mr = 24,160) were co-crystallized using ammonium sulfate as precipitant agent. The presence in the crystals of both components in the two-to-one stoichiometric ratio was demonstrated by electrophoresis, biological activity assays and crystallographic data. Crystals belong to the cubic space group I432 with cell parameter of 354 A and one complex particle per asymmetric unit. The solvent content of about 78% is favorable for a low resolution structural investigation. By exchanging H2O for D2O in mother liquors, advantage can be taken from contrast variation techniques with neutron radiations. Diffraction data to 20 A resolution were measured at five different contrasts, two of them being close to the theoretical matching point of RNA and protein in the presence of ammonium sulfate. The experimental extinction of the diffracted signal was observed to be close to 36% D2O, significantly different from the predicted value of 41%. The phenomenon can be explained by the existence of a large interface region between the two tRNAs and the enzyme. These parts of the molecules are hidden from the solvent and their protons are less easily exchangeable. Accessibility studies toward chemicals of tRNAAsp in solution and in the presence of synthetase are in agreement with such a model.

Amino Acyl-tRNA Synthetases↗

PubMed1983

Long-term biological consequences of nuclear war.

Subfreezing temperatures, low light levels, and high doses of ionizing and ultraviolet radiation extending for many months after a large-scale nuclear war could destroy the biological support systems of civilization, at least in the Northern Hemisphere. Productivity in natural and agricultural ecosystems could be severely restricted for a year or more. Postwar survivors would face starvation as well as freezing conditions in the dark and be exposed to near-lethal doses of radiation. If, as now seems possible, the Southern Hemisphere were affected also, global disruption of the biosphere could ensue. In any event, there would be severe consequences, even in the areas not affected directly, because of the interdependence of the world economy. In either case the extinction of a large fraction of the Earth's animals, plants, and microorganisms seems possible. The population size of Homo sapiens conceivably could be reduced to prehistoric levels or below, and extinction of the human species itself cannot be excluded.

Animals↗

PubMed1992

Phylogenetic analysis of alphaviruses in the Venezuelan equine encephalitis complex and identification of the source of epizootic viruses.

We studied the evolution of alphaviruses in the Venezuelan equine encephalitis (VEE) complex using phylogenetic analysis of RNA nucleotide sequences from limited portions of the nsP4, E1, and 3' untranslated genome regions of representative strains. The VEE complex constituted a monophyletic group of viruses (descended from a common ancestor); some serologic VEE varieties such as subtype III formed monophyletic groups while subtype I did not. Subtype II Everglades and variety ID enzootic viruses formed a monophyletic group which also included all epizootic variety IAB and IC VEE isolates. Everglades virus diverged from this ID lineage (colonized North America) ca. 100-150 years ago, followed by divergence of variety IAB and IC epizootic viruses. Variety IAB viruses probably emerged from the variety ID lineage once during the early part of this century, while variety IC viruses evolved at least two times. These results identify the source of epizootic VEE viruses as the variety ID enzootic virus lineage which occurs in northern South America and Panama. Even if variety IAB and IC viruses are extinct, recent, multiple emergences of epizootic viruses from an enzootic lineage suggests that other epizootic VEE viruses may evolve again in the future. The close genetic relationship of subtype II Everglades virus to the variety ID lineage also implies the potential for emergence of equine-virulent VEE viruses in Florida.

Base Sequence↗

PubMed2006

Dynamic-persistence of cooperation in public good games when group size is dynamic.

The evolution of cooperation is possible with a simple model of a population of agents that can move between groups. The agents play public good games within their group. The relative fitness of individuals within the whole population affects their number of offspring. Groups of cooperators evolve but over time are invaded by defectors which eventually results in the group's extinction. However, for small levels of migration and mutation, high levels of cooperation evolve at the population level. Thus, evolution of cooperation based on individual fitness without kin selection, indirect or direct reciprocity is possible. We provide an analysis of the parameters that affect cooperation, and describe the dynamics and distribution of population sizes over time.

Animals↗

PubMed1977

Restrictions on rotational and translational diffusion of pigment in the membranes of a rhabdomeric photoreceptor.

Individual, isolated rhabdoms from dark-adapted crayfish (Orconectes, Procambarus) were studied with a laterally incident microbeam that could be placed in single stacks of microvilli. Concentration gradients of metarhodopsin along the lengths of microvilli were produced by local bleaches, accomplished by irradiation with small spots of orange light at pH 9 in the presence of glutaraldehyde or formaldehyde. No subsequent redistribution of pigment was observed in the dark, indicating an absence of translational diffusion. On the basis of comparison with other systems, glutaraldehyde, but not formaldehyde (0.75%), would be expected to prevent diffusion of protein in the membrane. Under the same conditions photodichroism is observed, indicating an absence of free Brownian rotation. Photodichroism is larger in glutaraldehyde than in formaldehyde, suggesting that the bifunctional reagent quiets some molecular motion that is present after treatment with formaldehyde. Quantitative comparison of photodichroism with mathematical models indicates that the pigment absorption vectors are aligned within +/- 50 degrees of the microvillar axes and are tilted into the surface of the membrane at an average value of about 20 degrees. The photoconversion of rhodopsin to metarhodopsin is accompanied by an increase in molar extinction of about 20% at the lambda maxand a reorientation of the absorption vector by several degrees. The transition moment either tilts further into the membrane or loses some of its axial orientation, or both. The change in orientation is 3.5 time larger in formaldehyde than in glutaraldehyde.

Absorption↗

PubMedDate not supplied

The mutational meltdown in asexual populations.

Loss of fitness due to the accumulation of deleterious mutations appears to be inevitable in small, obligately asexual populations, as these are incapable of reconstituting highly fit genotypes by recombination or back mutation. The cumulative buildup of such mutations is expected to lead to an eventual reduction in population size, and this facilitates the chance accumulation of future mutations. This synergistic interaction between population size reduction and mutation accumulation leads to an extinction process known as the mutational meltdown, and provides a powerful explanation for the rarity of obligate asexuality. We give an overview of the theory of the mutational meltdown, showing how the process depends on the demographic properties of a population, the properties of mutations, and the relationship between fitness and number of mutations incurred.

Biological Evolution↗

PubMed2001

A test of whether rates of speciation were unusually high during the Cambrian radiation.

The Cambrian radiation represents an interval when nearly 20 animal phyla appear in the fossil record in a short geological time span; however, whether this radiation also represents a period of extremely rapid speciation remains unclear. Here, a stochastic framework is used to test the null hypothesis that diversity changes in one of the dominant Early Cambrian groups, the olenelloid trilobites, could be produced by tempos of speciation known to have operated during later time periods. Two continuous-time models, the Yule model and the birth and death process model, and one discrete-time model, the Bienaymé-Galton-Watson branching process model, were used. No statistical evidence for uniquely high rates of speciation during the radiation in these trilobites was found when the continuous-time models were used with low or moderate extinction rates, the rates typically associated with the Cambrian radiation, although the p values are fairly low or, in one case, significant when high extinction rates were used. However, rates of speciation were higher than the average Phanerozoic rates of speciation. The discrete-time model produced equivocal results: either rates were unusually high or the model is inapplicable during the Cambrian radiation. This suggests that there was nothing unique about evolutionary processes relating to the tempo of speciation during the Cambrian radiation.

Animals↗

PubMed2005

Dissecting the species-energy relationship.

Environmental energy availability can explain much of the spatial variation in species richness. Such species-energy relationships encompass a diverse range of forms, and there is intense debate concerning which of these predominate, and the factors promoting this diversity. Despite this there has been relatively little investigation of whether the form, and relative strength, of species-energy relationships varies with (i) the currency of energy availability that is used, and (ii) the ecological characteristics of the constituent species. Such investigations can, however, shed light on the causal mechanisms underlying species-energy relationships. We illustrate this using the British breeding avifauna. The strength of the species-energy relationship is dependent on the energy metric used, with species richness being more closely correlated with temperature than the Normalized Difference Vegetation Index, which is a strong correlate of net primary productivity. We find little evidence, however, for the thermoregulatory load hypothesis that high temperatures enable individuals to invest in growth and reproduction, rather than thermoregulation, increasing population sizes that buffer species from extinction. High levels of productive energy may also elevate population size, which is related to extinction risk by a negative decelerating function. Therefore, the rarest species should exhibit the strongest species-energy relationship. We find evidence to the contrary, together with little support for suggestions that high-energy availability elevates species richness by increasing the numbers of specialists or predators.

Animals↗

PubMed2006

Objectives for multiple-species conservation planning.

The first step in conservation planning is to identify objectives. Most stated objectives for conservation, such as to maximize biodiversity outcomes, are too vague to be useful within a decision-making framework. One way to clarify the issue is to define objectives in terms of the risk of extinction for multiple species. Although the assessment of extinction risk for single species is common, few researchers have formulated an objective function that combines the extinction risks of multiple species. We sought to translate the broad goal of maximizing the viability of species into explicit objectives for use in a decision-theoretic approach to conservation planning. We formulated several objective functions based on extinction risk across many species and illustrated the differences between these objectives with simple examples. Each objective function was the mathematical representation of an approach to conservation and emphasized different levels of threat. Our objectives included minimizing the joint probability of one or more extinctions, minimizing the expected number of extinctions, and minimizing the increase in risk of extinction from the best-case scenario. With objective functions based on joint probabilities of extinction across species, any correlations in extinction probabilities had to be known or the resultant decisions were potentially misleading. Additive objectives, such as the expected number of extinctions, did not produce the same anomalies. We demonstrated that the choice of objective function is central to the decision-making process because alternative objective functions can lead to a different ranking of management options. Therefore, decision makers need to think carefully in selecting and defining their conservation goals.

Conservation of Natural Resources↗

PubMed2000

Targets of extinction: identification of genes whose expression is repressed as a consequence of somatic fusion between cells representing basal and luminal mammary epithelial phenotypes.

The use of somatic cell hybrids has led to an increased understanding of the 'negative' regulation of cellular phenotype. Using somatic cell hybrids constructed between human breast cells that represent differing stages of malignancy but also display differing phenotypes from the same tissue, we present experimental results suggesting that luminal epithelial characteristics are controlled by repressive mechanisms. Fusion of HBL 100 cells, non-tumorigenic and characteristic of the basal cell lineage, with MCF-7 or MDA-MB-468 malignant breast cancer cells, characteristic of the luminal lineage, resulted in hybrid cells that displayed the phenotype of the HBL 100 cells. Using representational difference analysis, a panel of genes whose expression was repressed in the hybrid between HBL 100 and MDA-MB-468 was identified. This analysis revealed markers of luminal epithelial cells to be repressed, including Ep-CAM, cytokeratin 19 and E-cadherin. These markers were found to be coordinately re-expressed in variant hybrid cells indicating that the observed repression is reversible. Integrin (alpha)(v)(beta)(3) expression was found to be in mutual exclusivity to the luminal epithelial markers, thereby revealing a bidirectional 'switch' in the pattern of gene expression in this system. Finally, the expression of Ep-CAM was found to be lost in heterokaryons produced by fusion of HBL 100 and MCF-7 or MDA-MB-468 cells suggesting that the extinction of this gene in hybrid cells is the consequence of a trans-acting factor(s) synthesized by the HBL 100 cells. These data suggest that a number of markers of luminal cell differentiation in the mammary gland can be controlled through negative mechanisms and that such control of phenotype is highly coordinated.

Adenocarcinoma↗

PubMed2006

Operant conditioning of gill withdrawal in Aplysia.

A basic question in neuroscience is how different forms of learning are related. To further address that question, we examined whether gill withdrawal in Aplysia, which has already been studied extensively for neuronal mechanisms contributing to habituation, sensitization, and classical conditioning, also undergoes operant conditioning. Animals were run in pairs. During the initial training period, the contingent (experimental) animal received a siphon shock each time its gill relaxed below a criterion level, and the yoked control animal received a shock whenever the experimental animal did, regardless of its own gill position. This was followed by an extinction period when there was no shock, a retraining period when both animals were contingent, and another extinction period. The experimental animals spent more time with their gills contracted above the criterion level than did the control animals during each period, demonstrating operant conditioning. The type of gill behavior modified by learning shifted over time: the experimental animals had a larger increase in the frequency and duration of spontaneous contractions than did the control animals during the first but not the last extinction period and a larger increase in the level of tonic contraction during the last but not the first extinction period. Because many of the neurons controlling spontaneous and tonic gill withdrawal have already been identified, it should now be possible to examine the cellular locus and mechanism of operant conditioning and compare them with those for other forms of learning of the same behavior.

Animals↗

PubMed2006

Accumulation of deleterious mutations in small abiotic populations of RNA.

The accumulation of slightly deleterious mutations in populations leads to the buildup of a genetic load and can cause the extinction of populations of small size. Mutation-accumulation experiments have been used to study this process in a wide variety of organisms, yet the exact mutational underpinnings of genetic loads and their fitness consequences remain poorly characterized. Here, we use an abiotic system of RNA populations evolving continuously in vitro to examine the molecular events that can instigate a genetic load. By tracking the fitness decline of ligase ribozyme populations with bottleneck sizes between 100 and 3000 molecules, we detected the appearance and subsequent fixation of both slightly deleterious mutations and advantageous mutations. Smaller populations went extinct in significantly fewer generations than did larger ones, supporting the notion of a mutational meltdown. These data suggest that mutation accumulation was an important evolutionary force in the prebiotic RNA world and that mechanisms such as recombination to ameliorate genetic loads may have been in place early in the history of life.

Base Sequence↗

PubMed1991

[Medium-weight molecules and their indicator role in young children with acute pneumonia].

As many as 63 infants with acute pneumonia, 7 children with ARVI (bronchiolitis) and 28 normal children were examined. At the height of the clinical manifestations there was an increase of the level of medium-weight molecules in blood serum, correlating well with the disease gravity determined by the intensity of the toxic syndrome. The highest concentration of serum medium-weight molecules was demonstrable in toxic and purulent complications due to acute pneumonia. Meanwhile the level of medium-weight molecules, equal to or exceeding 0.6 Units extinction may be viewed as an unfavourable predictor. No relationship was discovered between the concentration of serum medium-weight molecules and the type of virus causative agent and respiratory tract inflammation.

Acute Disease↗

PubMed1975

Evolutionary history of the Cercopithecidae.

The application of cladistic methods (especially a concentration on shared derived rather than ancestral characters) permits the distinction of four dental and two cranial morphocytes among the Cercopithecidae. Comparison with fossils suggests that the Fayum parapithecids are not specially related to the Old World monkeys, while other undoubted Fayum 'hominoids' may share derived features with monkeys. Miocene Victoriapithecus 'species' may document a stage very close to the split between Colobinae and Cercopithecinae. Later African colobines appear to form a monophyletic group, more arboreal than the extinct European branch; Asian forms may be specially related to the latter. Among the Cercopithecinae, after a Miocene separation from the high-forest Cercopithecini, the Papionini divided into three groups: geladas, sub-Saharan Papio-related 'baboons' and Mediterranean-Eurasian macaque relatives; each of these underwent Plio-Pleistocene adaptive radiations and subsequent taxonomic diminution.

Africa↗

PubMed2001

Radiative decay engineering: biophysical and biomedical applications.

Fluorescence spectroscopy is a widely used research tool in biochemistry and molecular biology. Fluorescence has also become the dominant method enabling the revolution in medical diagnostics, DNA sequencing, and genomics. To date all the fluorescence observables, including spectral shifts, anisotropies, quantum yields, and lifetimes, have all been utilized in basic and applied uses of fluorescence. In this forward-looking article we describe a new opportunity in fluorescence, radiative decay engineering (RDE). By RDE we mean modifying the emission of fluorophores or chromophores by increasing or decreasing their radiative decay rates. In most fluorescence experiments the radiative rates are not changed because these rates depend on the extinction coefficient of the fluorophore. This intrinsic rate is not changed by quenching and is only weakly dependent on environmental effects. Spectral changes are usually caused by changes in the nonradiative rates resulting from quenching or resonance energy transfer. These processes affect the emission by providing additional routes for decay of the excited states without emission. In contrast to the relatively constant radiative rates in free solution, it is known that the radiative rates can be modified by placing the fluorophores at suitable distances from metallic surfaces and particles. This Review summarizes results from the physics literature which demonstrate the effects of metallic surfaces, colloids, or islands on increasing or decreasing emissive rates, increasing the quantum yields of low quantum yield chromophores, decreasing the lifetimes, and directing the typically isotropic emission in specific directions. These effects are not due to reflection of the emitted photons, but rather as the result of the fluorophore dipole interacting with free electrons in the metal. These interactions change the intensity and temporal and spatial distribution of the radiation. We describe the unusual effects expected from increases in the radiative rates with reference to intrinsic and extrinsic biochemical fluorophores. For instance, the decreased lifetime can result in an effective increase in photostability. Proximity to nearby metallic surfaces can also increase the local field and modify the rate of excitation. We predict that the appropriate localization of fluorophores near particles can result in usefully high emission from "nonfluorescent" molecules and million-fold increases in the number of photons observable from each fluorophore. We also describe how RDE can be applied to medical testing and biotechnology. As one example we predict that nearby metal surfaces can be used to increase the low intrinsic quantum yields of nucleic acids and make unlabeled DNA detectable using its intrinsic metal-enhanced fluorescence.

Energy Transfer↗

PubMed1997

The nitric oxide/superoxide assay. Insights into the biological chemistry of the NO/O-2. interaction.

Nitric oxide (NO) is a widespread signaling molecule involved in the regulation of an impressive spectrum of diverse cellular functions. Superoxide anions (O-2) not only contribute to the localization of NO action by rapid inactivation, but also give rise to the formation of the potentially toxic species peroxynitrite (ONOO-) and other reactive nitrogen oxide species. The chemistry and biological effect of ONOO- depend on the relative rates of formation of NO and O-2. However, the simultaneous quantification of NO and O-2 has not been achieved yet due to their high rate of interaction, which is almost diffusion-controlled. A sensitive spectrophotometric assay was developed for the simultaneous quantification of NO and O-2 in aqueous solution that is based on the NO-induced oxidation of oxyhemoglobin (oxyHb) to methemoglobin and the O-2-mediated reduction of ferricytochrome c. Using a photodiode array photometer, spectral changes of either reaction were analyzed, and appropriate wavelengths were identified for the simultaneous monitoring of absorbance changes of the individual reactions. oxyHb oxidation was followed at 541.2 nm (isosbestic wavelength for the conversion of ferri- to ferrocytochrome c), and ferricytochrome c reduction was followed at 465 nm (wavelength at which absorbance changes during oxyHb to methemoglobin conversion were negligible), using 525 nm as the isosbestic point for both reactions. At final concentrations of 20 microM ferricytochrome c and 5 microM oxyHb, the molar extinction coefficients were determined to be epsilon465-525 = 7.3 mM-1 cm-1 and epsilon541.2-525 = 6.6 mM-1 cm-1, respectively. The rates of formation of either NO or O-2 determined with the combined assay were virtually identical to those measured with the classical oxyhemoglobin and cytochrome c assays, respectively. The assay was successfully adapted to either kinetic or end point determination in a cuvette or continuous on-line measurement of both radicals in a flow-through system. Maximal assay sensitivity was approximately 25 nM for NO and O-2. Cross-reactivity with ONOO- was controlled for by the presence of L-methionine. Generation of NO from the NO donor spermine diazeniumdiolate could be reliably quantified in the presence and absence of low, equimolar, and high flux rates of O-2. Likewise, O-2 enzymatically generated from hypoxanthine/xanthine oxidase could be specifically quantified with no difference in absolute rates in the presence or absence of concomitant NO generation at different flux rates. Nonenzymatic decomposition of 3-morpholinosydnonimine hydrochloride (100 microM) in phosphate buffer, pH 7.4 (37 degrees C), was found to be associated with almost stoichiometric production of NO and O-2 (1.24 microM NO/min and 1.12 microM O-2/min). Assay selectivity and applicability to biological systems were demonstrated in cultured endothelial cells and isolated aortic tissue using calcium ionophore and NADH for stimulation of NO and O-2 formation, respectively. Based on these data, a computer model was elaborated that successfully predicts the reaction of NO and O-2 with hemoprotein and may thus help to further elucidate these reactions. In conclusion, the nitric oxide/superoxide assay allows the specific, sensitive, and simultaneous detection of NO and O-2. The simulation model developed also allows the reliable prediction of the reaction between NO and O-2 as well as their kinetic interaction with other biomolecules. These new analytical tools will help to gain further insight into the physiological and pathophysiological significance of the formation of these radicals in cell homeostasis.

Cytochrome c Group↗