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Some problems of molecular biology of poliovirus infection relevant to pathogenesis, viral spread and evolution.

Molecular mechanisms of poliovirus reproduction in the human gut remain largely unexplored. Nevertheless, there are grounds to believe that the virus spreads from cell to cell, like that from person to person during natural circulation, and involves a relatively small proportion of the highly heterogeneous viral population generated by the previous host. This mechanism of random sampling is responsible for the majority of fixed mutations, and contributes to the maintenance of a certain level of viral fitness (virulence). In the long term, random sampling may lead to the decrease in fitness and even to extinction of some viral evolutionary branches, explaining cases of self-limiting poliovirus infection in immunodeficient patients. A low propensity of the Sabin viruses for natural circulation may also be a related phenomenon. The trend to decrease in fitness may be interrupted by the appearance of rare, fitter (more virulent) variants, which may be responsible for poliomyelitis outbreaks caused by wild type virus, and for the development of paralytic disease in chronic carriers of the Sabin vaccine. All these evolutionary events are largely stochastic and hence are unpredictable in principle.

Digestive System↗

[The behavioral characteristics of rats induced by partial degeneration of the hippocampal cholinergic neurons].

The effects of intraventricular administration of ethylcholine aziridinium ion (AF64A) were studied in male Wistar rats. Bilateral injections of AF64A (3 nm/3 mcl) reduced the reactions to biological alarm signal and produced a decrease in the open-field activity 3 weeks after this lesion. The lesioned rats also displayed deficit in retention of a passive avoidance task.

Animals↗

Continuous spectrophotometric assay for ascorbate oxidase based on a novel chromophoric substrate, 2-aminoascorbic acid.

Recently, we reported the development of a sensitive continuous spectrophotometric assay for the ascorbate-dependent mammalian enzyme dopamine beta-monooxygenase based on the novel chromophoric electron donor 2-aminoascorbic acid [K. Wimalasena and D.S. Wimalasena (1991) Anal. Biochem. 197, 353-361]. We now report that ascorbate oxidase (EC 1.10.3.3, L-ascorbate:O2 oxidoreductase) also catalyzes the oxidation of 2-aminoascorbic acid to chromophoric 2,2'-nitrilodi-2(2')-deoxy-L-ascorbic acid (red pigment). The reaction is kinetically well behaved, displaying the expected stoichiometry for an oxidase-catalyzed reaction with respect to oxygen and the oxidation product (red pigment), demonstrating that 2-aminoascorbic acid is a well-behaved alternative substrate for the enzyme. Ascorbate oxidase is a very efficient enzyme toward its natural substrate, ascorbic acid. Although 2-amino-ascorbic acid is a significantly weak substrate for the enzyme in comparison to ascorbic acid, as indicated by the apparent initial rate kinetic parameters, the high extinction coefficient of the red pigment under our assay conditions suggests that this novel reactivity of the enzyme could be used to design a sensitive, convenient, and continuous spectrophotometric assay for ascorbate oxidase. While this assay is more convenient than the existing oxygen monitor assay, its adaptability to measure the activity of the enzyme in the immobilized form may be helpful in the development of technologies for the automated detection of ascorbic acid in biological fluids for industrial or clinical applications. In addition, this novel reactivity of the enzyme may be used to examine the substrate specificity and the mechanism of action of the enzyme.

Ascorbate Oxidase↗

Sorption of 17beta-estradiol and 17alpha-ethinylestradiol by colloidal organic carbon derived from biological wastewater treatment systems.

Sorption coefficients (K(COC)) between 17beta-estradiol (E2), 17alpha-ethinylestradiol (EE2) and size-fractionated colloidal organic carbon (COC) derived from two biological wastewater treatment facilities were quantified by fluorescence quenching. The two wastewater treatment systems included a full-scale activated sludge system (FSAS) and a membrane bioreactor (MBR). The K(COC) coefficients were highly variable and ranged between (<1 to 179) x 10(3) L/kgCOC for E2 and (<1 to 430) x 10(3) L/kgCOC for EE2 and were higher than expected from the analytes octanol-water partition coefficient. Correlations between the molar extinction coefficients measured at 280 nm (e280) and K(COC) coefficients were weak but stronger for E2 compared to EE2. Attempts at correlating sorption behavior with colloidal protein and polysaccharide concentrations were only marginally successful (r2 approximately 0.4). These low correlations suggest that aromatic content, protein, or polysaccharide concentration can not adequately explain E2 and EE2 sorption behavior to COC and that other fractions of the organic matter pool play an important role in binding. A substantial portion of the aqueous E2 and EE2 concentrations (up to 60%) may be associated with colloidal material, suggesting that COC may play a role in the fate and transport of E2 and EE2 during the activated sludge process.

Adsorption↗

Dispensable and indispensable genes in an ameiotic fish, the Amazon molly Poecilia formosa.

All-female vertebrates are excellent model systems for studying many evolutionary problems. One of these is the Amazon molly. In this review, three aspects of its biology are discussed: (1) An important question is how dispensable genes, such as all male coding genes, evolve in this species. A number of studies found that most of these genes remain remarkably stable and functional. (2) The gynogenetic Amazon mollies have to live in sympatry with males of a gonochoristic species, because sperm are needed to trigger embryogenesis. Yet, Amazon mollies cannot replace their sexual competitors, because this would lead to their own extinction. Studies on the behavior of Amazon mollies and their sperm-donor species indicate that a number of behavior patterns stabilize the mating system by providing Amazon mollies with the copulations they need to reproduce. (3) The age of Amazon mollies has been estimated to be approximately 100,000 years. This is older than predicted by some theoretical models. In Amazon mollies two ways to occasionally incorporate fresh genetic material have evolved. One way is to add one complete set of paternal chromosomes, which, in nature, leads to stable triploid lineages. The second way is the incorporation of minute, centromere-containing microchromosomes. The evolutionary impact of these phenomena, however, is not resolved so far and needs further study.

Animals↗

Co-operation and defection: playing the field in virus dynamics.

A previous model (Szathmáry, 1992) is further developed for the dynamics of standard (V) and defective interfering (DI) viruses. The crucial retained element is the incorporation of population structure in the form of a complete distribution of cells infected by particles differing in number. New elements are: the non-linear shared benefit from the contribution of Vs to the group of viruses infecting the same cell (synergistic at low numbers, diminishing returns at high numbers, respectively); a dynamics for the total number of particles (V and DI); and the possibility of extinction if the frequency of Vs is small enough. In evolutionary genetical terms this is a frequency- and density-dependent evolutionary game. A crucial result is retained: coexistence of Vs and DIs is possible provided the multiplicity of infection (hence the size of the coinfection group) is large enough. Phase portraits and vector-field plots for a continuous-time and numerical solutions for a corresponding discrete-time case are presented. The latter reflect the basic features of serial, undiluted passage. The causes for two possible means of extinction (low initial frequency of Vs, and very high vigour of Vs) are revealed: the appearance of high amplitude fluctuations. Coexistence can apparently be ensured by stable points, periodic behaviour, or strange attractors. The paper clarifies the dynamical background of cycles found experimentally in V-DI systems.

Biological Evolution↗

Novel moment closure approximations in stochastic epidemics.

Moment closure approximations are used to provide analytic approximations to non-linear stochastic population models. They often provide insights into model behaviour and help validate simulation results. However, existing closure schemes typically fail in situations where the population distribution is highly skewed or extinctions occur. In this study we address these problems by introducing novel second- and third-order moment closure approximations which we apply to the stochastic SI and SIS epidemic models. In the case of the SI model, which has a highly skewed distribution of infection, we develop a second-order approximation based on the beta-binomial distribution. In addition, a closure approximation based on mixture distribution is developed in order to capture the behaviour of the stochastic SIS model around the threshold between persistence and extinction. This mixture approximation comprises a probability distribution designed to capture the quasi-equilibrium probabilities of the system and a probability mass at 0 which represents the probability of extinction. Two third-order versions of this mixture approximation are considered in which the log-normal and the beta-binomial are used to model the quasi-equilibrium distribution. Comparison with simulation results shows: (1) the beta-binomial approximation is flexible in shape and matches the skewness predicted by simulation as shown by the stochastic SI model and (2) mixture approximations are able to predict transient and extinction behaviour as shown by the stochastic SIS model, in marked contrast with existing approaches. We also apply our mixture approximation to approximate a likelihood function and carry out point and interval parameter estimation.

Computer Simulation↗

Behavioral plasticity and virus propagation: the FIV-cat population example.

A new theoretical approach is proposed to investigate the effect of intra-individual variability in behavior on the spread of directly transmitted diseases within host populations. The classical hawk-dove game is used to describe interactions between individuals on a fast time scale (the day). Individuals may exhibit both tactics according to their own experience, to environment conditions, and to the opponent. They are not able to recognize the epidemiological state of their opponents. This fast-time part of the model is coupled to a classical compartmental epidemic model describing the demography of the population and the transmission of the disease from an infected individual to a healthy one on a slow time scale (the year). The model is applied to the case of feline immunodeficiency virus (FIV)-domestic cat population system. Our model gives rise to different predictions according to values of cost and gain due to fights: extinction of the epidemic, FIV endemicity at low, intermediate and high prevalence. These predictions are in good agreement with results from domestic cat populations living in different environmental conditions.

Animals↗

Photophysical studies of oxicam group of NSAIDs: piroxicam, meloxicam and tenoxicam.

Oxicam group of non steroidal anti-inflammatory drugs has been chosen as a prototype molecular group that shows diverse biological functions and dynamic structural features. Photophysical studies of three drugs from this group viz., piroxicam, meloxicam and tenoxicam have been carried out in different solvents with varying polarity, H-bond character and viscosity. The spectral responses of different prototropic forms of these drugs towards varying solvent parameters have been studied, with the aim to characterize their interaction in biomimetic environment non-invasively. The nature of the lowest transition has been identified. The extinction coefficient, quantum yield and viscosity dependence on the nature of the solvents, all indicate the extreme sensitivity of these drugs to their microenvironment.

Anti-Inflammatory Agents, Non-Steroidal↗

Calculated absorption and scattering properties of gold nanoparticles of different size, shape, and composition: applications in biological imaging and biomedicine.

The selection of nanoparticles for achieving efficient contrast for biological and cell imaging applications, as well as for photothermal therapeutic applications, is based on the optical properties of the nanoparticles. We use Mie theory and discrete dipole approximation method to calculate absorption and scattering efficiencies and optical resonance wavelengths for three commonly used classes of nanoparticles: gold nanospheres, silica-gold nanoshells, and gold nanorods. The calculated spectra clearly reflect the well-known dependence of nanoparticle optical properties viz. the resonance wavelength, the extinction cross-section, and the ratio of scattering to absorption, on the nanoparticle dimensions. A systematic quantitative study of the various trends is presented. By increasing the size of gold nanospheres from 20 to 80 nm, the magnitude of extinction as well as the relative contribution of scattering to the extinction rapidly increases. Gold nanospheres in the size range commonly employed ( approximately 40 nm) show an absorption cross-section 5 orders higher than conventional absorbing dyes, while the magnitude of light scattering by 80-nm gold nanospheres is 5 orders higher than the light emission from strongly fluorescing dyes. The variation in the plasmon wavelength maximum of nanospheres, i.e., from approximately 520 to 550 nm, is however too limited to be useful for in vivo applications. Gold nanoshells are found to have optical cross-sections comparable to and even higher than the nanospheres. Additionally, their optical resonances lie favorably in the near-infrared region. The resonance wavelength can be rapidly increased by either increasing the total nanoshell size or increasing the ratio of the core-to-shell radius. The total extinction of nanoshells shows a linear dependence on their total size, however, it is independent of the core/shell radius ratio. The relative scattering contribution to the extinction can be rapidly increased by increasing the nanoshell size or decreasing the ratio of the core/shell radius. Gold nanorods show optical cross-sections comparable to nanospheres and nanoshells, however, at much smaller effective size. Their optical resonance can be linearly tuned across the near-infrared region by changing either the effective size or the aspect ratio of the nanorods. The total extinction as well as the relative scattering contribution increases rapidly with the effective size, however, they are independent of the aspect ratio. To compare the effectiveness of nanoparticles of different sizes for real biomedical applications, size-normalized optical cross-sections or per micron coefficients are calculated. Gold nanorods show per micron absorption and scattering coefficients that are an order of magnitude higher than those for nanoshells and nanospheres. While nanorods with a higher aspect ratio along with a smaller effective radius are the best photoabsorbing nanoparticles, the highest scattering contrast for imaging applications is obtained from nanorods of high aspect ratio with a larger effective radius.

Absorption↗

Prehistoric birds from New Ireland, Papua New Guinea: extinctions on a large Melanesian island.

At least 50 species of birds are represented in 241 bird bones from five late Pleistocene and Holocene archaeological sites on New Ireland (Bismarck Archipelago, Papua New Guinea). The bones include only two of seabirds and none of migrant shorebirds or introduced species. Of the 50 species, at least 12 (petrel, hawk, megapode, quail, four rails, cockatoo, two owls, and crow) are not part of the current avifauna and have not been recorded previously from New Ireland. Larger samples of bones undoubtedly would indicate more extirpated species and refine the chronology of extinction. Humans have lived on New Ireland for ca. 35,000 years, whereas most of the identified bones are 15,000 to 6,000 years old. It is suspected that most or all of New Ireland's avian extinction was anthropogenic, but this suspicion remains undetermined. Our data show that significant prehistoric losses of birds, which are well documented on Pacific islands more remote than New Ireland, occurred also on large, high, mostly forested islands close to New Guinea.

Animals↗

Caged cyclic ADP-ribose. Synthesis and use.

Cyclic ADP-ribose (cADPR) is a recently discovered cyclic nucleotide with Ca2+ mobilizing activity. Caged cADPR was synthesized by reacting cADPR with 2-nitrophenethyldiazoethane. Elemental analyses, 1H NMR, and extinction coefficient measurements indicate that the product contains only one caging group. Anion exchange high pressure liquid chromatography separated caged cADPR into two forms, which most likely represent isomers. Both forms could be uncaged with equal efficiency by UV exposure to regenerate cADPR. Photolysis of caged cADPR was accomplished effectively with a spectrofluorimeter. The efficiency of uncaging depended on wavelength with UV light shorter than about 320 nm being the most effective. Caged cADPR was biologically inactive and could induce Ca2+ release from sea urchin egg homogenates only after photolysis. Specificity of the Ca2+ release was shown by inhibition by 8-amino-cADPR, a specific antagonist of cADPR. To demonstrate its utility in live cells, caged cADPR was microinjected into sea urchin eggs. Photolysis using a mercury light source effectively regenerated cADPR and resulted in Ca2+ mobilization and activation of cortical exocytosis in the eggs.

ADP-ribosyl Cyclase↗

An improved procedure for the assay of available lysine and methionine in feedstuffs using Tetrahymena pyriformis W.

1. A study was made of the assay of available lysine and available methionine using Tetrahymena pyriformis W, as applied to a variety of protein-rich feedstuffs. 2. Results were strongly influenced by the conditions under which the analyses were done. With most of the test samples predigestion with papain caused a large increase in the values obtained. 3. An improved assay procedure was developed which included enzymic predigestion of the test samples, "all-in" sterilization of the medium constituents, and measurement of growth from extinction values. It gave results for available lysine that were broadly similar to those obtained in growth tests with rats, and in chemical tests by the method of Carpenter (1960). Values for available methionine agreed closely with those obtained in microbiological tests with Streptococcus zymogenes.

Animal Feed↗

Predicting which species will benefit from corridors in fragmented landscapes from population growth models.

Connecting isolated patches of habitat in fragmented landscapes with corridors is a popular conservation strategy. This strategy is also controversial in large part because of uncertainty about what characteristics of a species and its environment promote corridor use. In this article we address the question, For what types of species will populations benefit from corridors? We asked this question using a model of two logistically growing populations connected by migration in which both emigration and migration success were determined by the presence or absence of a corridor. We found that in the short run (e.g., during recovery from disaster), corridors are most effective for species with fast-growing populations that have low survivorship when dispersing through unsuitable (matrix) habitat. We also found that emigration rates and habitat-specific mortality rates are key determinants of the effects of corridors on population size. In the long term, corridors are most likely to benefit species with slow-growing populations that have low survivorship when dispersing through matrix habitat. Our results confirm the major conclusions from previous empirical studies of corridor benefits. However, most studies fail to consider the most appropriate questions to determine the potential benefits of habitat corridors. First, what is the time scale of the conservation goal? Corridors have positive effects on different suites of species in the short and long term. Second, is the major threat of local extinction due to sustained population decline or boom-bust cycles? Third, what is the migration rate through the matrix? Fourth, what fraction of migrants dispersing through the matrix successfully immigrate to another patch?

Conservation of Natural Resources↗

The accumulation of deleterious mutations within the frozen niche variation hypothesis.

The frozen niche variation hypothesis proposes that asexual clones exploit a fraction of a total resource niche available to the sexual population from which they arise. Differences in niche breadth may allow a period of coexistence between a sexual population and the faster reproducing asexual clones. Here, we model the longer term threat to the persistence of the sexual population from an accumulation of clonal diversity, balanced by the cost to the asexual population resulting from a faster rate of accumulation of deleterious mutations. We use Monte-Carlo simulations to quantify the interaction of niche breadth with accumulating deleterious mutations. These two mechanisms may act synergistically to prevent the extinction of the sexual population, given: (1) sufficient genetic variation, and consequently niche breadth, in the sexual population; (2) a relatively slow rate of accumulation of genetic diversity in the clonal population; (3) synergistic epistasis in the accumulation of deleterious mutations.

Biological Evolution↗

Coherence and conservation.

A principal aim of current conservation policy is to reduce the impact of habitat fragmentation. Conservation corridors may achieve this goal by facilitating movement among isolated patches, but there is a risk that increased connectivity could synchronize local population fluctuations (causing coherent oscillations) and thereby increase the danger of global extinction. We identify general conditions under which populations can or cannot undergo coherent oscillations, and we relate these conditions to local and global extinction probabilities. We suggest a simple method to explore the potential success of conservation corridors and, more generally, any manipulations of dispersal patterns that aim to protect threatened species or control pests.

Animals↗

Evolution of subgroup A respiratory syncytial virus: evidence for progressive accumulation of amino acid changes in the attachment protein.

The variability of the attachment (G) proteins of 48 subgroup A isolates of respiratory syncytial virus (RSV) isolated over 38 years has been examined. Nucleotide sequences of two variable regions of the G protein genes were determined following amplification by PCR. The isolates showed temporal rather than geographical clustering, and there was evidence for progressive accumulation of amino acid changes at an average rate of approximately 0.25% per year estimated over the entire protein. The cocirculation of lineages of RSV at present appears to be the result of a process of evolution and survival of particular genotypes and the extinction of others. Analysis of reactivity of the isolates with monoclonal antibodies showed that their antigenic profiles closely paralleled their relatedness by nucleotide sequence, suggesting that antigenic drift due to immune selection may be occurring.

Amino Acid Sequence↗

A fecundity to mortality ratio, population size variability and the chance for a mammal species to be listed on the red list.

How is a species' propensity to vary in size over time related to its chances to be listed on the Red List (Red Book), that is to face the risk of extinction? Here I suggest that the linkage between the range of population fluctuations and chance of listing may be established on the basis of the ratio of species' annual fecundity to annual mortality of adults, B/M. For 23 mammalian species inhabiting the vast tracts of Western Siberia, the range of population fluctuations is found to be equal or at least proportional to B/M. Further, this ratio is estimated for a larger set of 90 mammalian species from the territory and coastal waters of the former Soviet Union, of which 25 species are listed in the Red Book of the USSR. The distribution of the Red Book species over the gradient of B/M is clearly non-uniform: most of them have low B/M, which leads to a negative relationship between chance of listing and B/M. The positive relation between population size variability and B/M and the negative relation between chance of listing and B/M suggest the resulting negative relation between chance of listing and population size variability. Both the positive and the negative relations of, respectively, population size variability and chance of listing on B/M are logically justified since B/M is a measure of the population growth rate: it is the total lifetime offspring and an upper estimate of the growth rate per generation time. Fast-growing, more resilient species tend to be more resistant to extinction and hence to have low chance of listing, but simultaneously are able to fluctuate widely. Thus, so long as population growth rate affects both chance of listing and population size variability, high variability implies low chance of listing.

Animals↗