The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

We investigate how scale-free (SF) and Erd?s-Rényi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SF_in topologies, that is SF topology for incoming nodes and ER topology for outgoing nodes, are significantly more evolvable towards specific oscillatory targets than networks with ER topology for both incoming and outgoing nodes. Similar results are found for networks with SF_both and SF_out topologies. The functionality of the SF_out topology, which most closely resembles the structure of biological gene networks (Babu et al., 2004), is compared to the ER topology in further detail through an extension to multiple target outputs, with either an oscillatory or a non-oscillatory nature. For multiple oscillatory targets of the same length, the differences between SF_out and ER networks are enhanced, but for non-oscillatory targets both types of networks show fairly similar evolvability. We find that SF networks generate oscillations much more easily than ER networks do, and this may explain why SF networks are more evolvable than ER networks are for oscillatory phenotypes. In spite of their greater evolvability, we find that networks with SF_out topologies are also more robust to mutations (mutational robustness) than ER networks. Furthermore, the SF_out topologies are more robust to changes in initial conditions (environmental robustness). For both topologies, we find that once a population of networks has reached the target state, further neutral evolution can lead to an increase in both the mutational robustness and the environmental robustness to changes in initial conditions.     

Effects of population size and mutation rate on the evolution of mutational robustness

It is often assumed that the efficiency of selection for mutational robustness would be proportional to mutation rate and population size, thus being inefficient in small populations. However, Krakauer and Plotkin (2002) hypothesized that selection in small populations would favor robustness mechanisms, such as redundancy, that mask the effect of deleterious mutations. In large populations, by contrast, selection is more effective at removing deleterious mutants and fitness would be improved by eliminating mechanisms that mask the effect of deleterious mutations and thus impede their removal. Here, we test whether these predictions are supported in experiments with evolving populations of digital organisms. Digital organisms are self-replicating programs that inhabit a virtual world inside a computer. Like their organic counterparts, digital organisms mutate, compete, evolve, and adapt by natural selection to their environment. In this study, 160 populations evolved at different combinations of mutation rate and population size. After 10(4) generations, we measured the mutational robustness of the most abundant genotype in each population. Mutational robustness tended to increase with mutation rate and to decline with population size, although the dependence with population size was in part mediated by a negative relationship between fitness and robustness. These results are independent of whether genomes were constrained to their original length or allowed to change in size.     

The effect of trait type and strength of selection on heritability and evolvability in an island bird population

The heritability (h²) of fitness traits is often low. Although this has been attributed to directional selection having eroded genetic variation in direct proportion to the strength of selection, heritability does not necessarily reflect a trait's additive genetic variance and evolutionary potential (“evolvability”). Recent studies suggest that the low h² of fitness traits in wild populations is caused not by a paucity of additive genetic variance (V_A) but by greater environmental or nonadditive genetic variance (V_R). We examined the relationship between h² and variance‐standardized selection intensities (i or β_σ), and between evolvability (I_A:V_A divided by squared phenotypic trait mean) and mean‐standardized selection gradients (β_μ). Using 24 years of data from an island population of Savannah sparrows, we show that, across diverse traits, h² declines with the strength of selection, whereas I_A and I_R (V_R divided by squared trait mean) are independent of the strength of selection. Within trait types (morphological, reproductive, life‐history), h², I_A, and I_R are all independent of the strength of selection. This indicates that certain traits have low heritability because of increased residual variance due to the age at which they are expressed or the multiple factors influencing their expression, rather than their association with fitness.     

The effect of diphylic compounds on the transport of metabolites and cations in eukaryotic cells

The effect of DMSO, glycerol, PEG, PVP on passive and active transport of metabolites and cations to the cells of Ehrlich ascites carcinoma and erythrocytes has been investigated. The data indicating the stimulation or reversible inhibition of amino acid, nucleosides transport dependent on concentration of diphylic compounds have been shown. The inhibitory mechanisms of processes of metabolite and cation transport have been discussed.     

生境破坏的模式对集合种群动态和续存的影响

构建了空间关联的集合种群模型,该模型不但包含了种群的空间结构信息,而且引入了破坏生境的全局密度和局部密度两个指标,它们描述了破坏生境的模式.模型揭示了破坏生境的空间分布格局复杂地影响了集合种群的动态和续存,破坏和未破坏生境斑块的均匀混合不利于集合种群的增长和续存,而生境类型聚集分布可以促进集合种群的快速增长和长期续存;对于两种斑块类型相对均匀混合的生境来说,均匀场假设可能会高估集合种群的续存,对于相对斑块类型高度聚集的生境,均匀场假设可能会低估集合种群的续存;物种的迁移范围也会影响集合种群的续存,迁移范围越大的物种越容易抵御生境的破坏而免遭灭绝.这意味着在生物保护中不能仅仅考虑生境的恢复和斑块质量的改善,生境结构的构建也是很重要的,加强生境斑块之间的连通性也有利于物种的长期续存.     

Characterization of stem cells and cancer cells on the basis of gene expression profile stability, plasticity, and robustness: dynamical systems theory of gene expressions under cell-cell interaction explains mutational robustness of differentiated cells and suggests how cancer cells emerge

Here I present and discuss a model that, among other things, appears able to describe the dynamics of cancer cell origin from the perspective of stable and unstable gene expression profiles. In identifying such aberrant gene expression profiles as lying outside the normal stable states attracted through development and normal cell differentiation, the hypothesis explains why cancer cells accumulate mutations, to which they are not robust, and why these mutations create a new stable state far from the normal gene expression profile space. Such cells are in strong contrast with normal cell types that appeared as an attractor state in the gene expression dynamical system under cell-cell interaction and achieved robustness to noise through evolution, which in turn also conferred robustness to mutation. In complex gene regulation networks, other aberrant cellular states lacking such high robustness are expected to remain, which would correspond to cancer cells.     

The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available datasets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore the biological factors that can explain this observation. We find that observed patterns of differences in the neutrality index, polymorphism, and divergence are not caused by differences in mutational bias. They can, however, be explained by a combination of a small fraction of neutral amino acid sites, weak selection acting on most amino acid mutations, and differences in effective population size among taxa.     

The effect of cytisine on mRNA transport in the cytoplasm of eukaryotic cells (plants and animals)

The action of alkaloid cytisine on protein biosynthesis in eukaryotic cells was studied. It was shown that the alkaloid had no effect on mRNA translation. Cytisine inhibited the release of mRNP particles from rat liver and wheat embryos nuclei. Sedimentation properties and distribution in CsCl gradient of the material extracted from alkaloid-treated nuclei did not differ from control one and were similar to informosomes from animal and plant cells described earlier. The main part of mRNA with sedimentation coefficients 14-18S, capable for translation in the cytoplasm is retained in alkaloid-treated nuclei.     

The effect of coil phenotypes and genotypes on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: implications for the evolution of sinistral snails

Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency‐dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (< 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency‐dependent selection may be overcome by a negative frequency‐dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act.     

The evolution of conspecific gamete precedence and its effect on reinforcement

Conspecific gamete precedence, the usage of conspecific sperm by a female that mates with both a conspecific and a heterospecific male, has been found in many taxa. We construct a population genetic model to examine the evolution of conspecific gamete precedence and its coevolution with premating isolation in the process of reinforcement. Our findings suggest that conspecific gamete precedence can evolve via a process very similar to reinforcement. We explore the nature of the selection against hybridization necessary to drive this evolution. Moreover, our results confirm the prediction of Marshall et al. (Trends Ecol. Evol. 2002;17:558-563) that conspecific gamete precedence will inhibit the evolution of reinforcement between two species. We further find that reinforcement will inhibit the evolution of conspecific gamete precedence. Both reinforcement and conspecific gamete precedence increase reproductive isolation and contribute to the process of speciation. We discuss factors that may affect which of these phenomena are likely to become predominant between incipient species.     

The effects of flow and stream characteristics on the variation in freshwater mussel growth in a Southeast US river basin

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The effect of donor age on the in vitro life span of cultured human arterial smooth-muscle cells

Summary The number of population doublings of cultured human arterial smooth-muscle cells decreased as a function of donor age (0.5 to 82 years). Cells from older donors als showed longer latent periods for outgrowth from explants. These results extend other comprable observations with human skin fibroblasts to another cell type, and may have relevance to the pathogenesis of atherosclerosis with aging in vivo. This study was supported by a reserach program project grant (AG00299) from the National Institutes of Health.     

The effect of light and darkness on hatching in the pomacentrid Abudefduf saxatilis

Synopsis Reports that pomacentrid embryos hatch after dusk are confirmed by photic manipulation of sergeant major eggs. Embryos placed in the dark for 20 minutes or longer prior to their normal hatching after sunset hatched, whereas controls held in light did not hatch. Percent of hatched embryos correlated with increasing exposure to darkness up to one hour after which no further improvement in hatching was observed. Embryos maintained in continuous light during their normal twilight hatching period did not hatch. Also, embryos exposed to 60 minutes of darkness, if interrupted by one minute of light every 10 minutes did not hatch. The percent hatch in dark treatments varied significantly between nests and, in some treatments, correlated negatively with the size of the egg clumps (number of eggs per clump) tested. To initiate hatching in the presence of light required intensities of 0.03 lux or less. These low intensities are not reached until about 20 minutes after sunset on the reef where the embryos occur. We conclude that hatching for some embryos occurs about 30 minutes after sunset but for most is not completed until at least one hour after sunset. Hatching therefore takes place at a time long after potential diurnal fish predators have refuged in the reef structure.     

Exopolysaccharides produced by Lactobacillus and Bifidobacterium strains abrogate in vitro the cytotoxic effect of bacterial toxins on eukaryotic cells

Aims: To evaluate the capability of the exopolysaccharides (EPS) produced by lactobacilli and bifidobacteria from human and dairy origin to antagonize the cytotoxic effect of bacterial toxins. Methods and Results: The cytotoxicity of Bacillus cereus extracellular factors on Caco‐2 colonocytes in the presence/absence of the EPS was determined by measuring the integrity of the tissue monolayer and the damage to the cell membrane (extracellular lactate dehydrogenase activity). Additionally, the protective effect of EPS against the haemolytic activity of the streptolysin‐O was evaluated on rabbit erythrocytes. The EPS produced by Bifidobacterium animalis ssp. lactis A1 and IPLA‐R1, Bifidobacterium longum NB667 and Lactobacillus rhamnosus GG were able to counteract the toxic effect of bacterial toxins on the eukaryotic cells at 1 mg ml^?1 EPS concentration. The EPS A1 was the most effective in counteracting the effect of B. cereus toxins on colonocytes, even at lower doses (0·5 mg ml^?1), whereas EPS NB667 elicited the highest haemolysis reduction on erythrocytes. Conclusions: The production of EPS by lactobacilli and bifidobacteria could antagonize the toxicity of bacterial pathogens, this effect being EPS and biological marker dependent. Significance and Impact of the Study: This work allows gaining insight about the mechanisms that probiotics could exert to improve the host health.     

The effect of food quantity and quality on the growth,birth-rate and longevity of Daphnia hyalina Leydig

To study experimentally the relation between zooplankton and phytoplankton, laboratory cultures of Daphnia hyalina Leydig were set up. The combined influence of food quality and quantity on growth, birth-rate and longevity was measured. The effect of seven different food regimes was tested. Natural unfiltered lake water from the eutrophic lake Tjeukemeer was used in one regime. The food value of the natural unfiltered lake water appeared to be relatively low, which was most likely caused by the abundance of large sized algae in the lake water.     

The effect of amino density on the attachment, migration, and differentiation of rat neural stem cells In Vitro

Artificial extracellular matrices play important roles in the regulation of stem cell behavior. To generate materials for tissue engineering, active functional groups, such as amino, carboxyl, and hydroxyl, are often introduced to change the properties of the biomaterial surface. In this study, we chemically modified coverslips to create surfaces with different amino densities and investigated the adhesion, migration, and differentiation of neural stem cells (NSCs) under serum-free culture conditions. We observed that a higher amino density significantly promoted NSCs attachment, enhanced neuronal differentiation and promoted excitatory synapse formation in vitro. These results indicate that the amino density significantly affected the biological behavior of NSCs. Thus, the density and impact of functional groups in extracellular matrices should be considered in the research and development of materials for tissue engineering.     

The effect of adapting speed,duration, and distance on the tactile motion aftereffect

We investigated the effect of adapting speed, duration, and distance on the frequency of occurrence, duration, and vividness of the tactile motion aftereffect (tMAE). Using a cylindrical drum with a patterned surface we adapted the glabrous surface of the right hand at two speeds (14 and 28 cm/s) and three durations (60, 120, and 240 s). Distance was explored in the interaction of adapting speed and duration. The results showed that the frequency of occurrence, duration, and vividness of the tMAE increased with adapting speed. There was also a positive relationship between adapting duration and the frequency of occurrence, but not the duration or vividness, of the illusion. Distance was only a factor when it came to the duration of the tMAE. Taken together, these results show the importance of adapting parameters, particularly speed, on the tMAE.     

The effect of relatedness on likelihood ratios and the use of conservative estimates

DNA profiling can be used to identify criminals through their DNA matching that left at the scene of a crime. The strength of the evidence supplied by a match in DNA profiles is given by the likelihood ratio. This, in turn, depends upon the probability that a match would be produced if the suspect is innocent. This probability could be strongly affected by the possibility of relatedness between the suspect and the true source of the scene-of-crime DNA profile. Methods are shown that allow for the possibility of such relatedness, arising either through population substructure or through a family relationship. Uncertainties about the likelihood ratio have been taken as grounds for the use of very conservative estimates of this quantity. The use of such conservative estimates can be shown to be neither necessary nor harmless.Editor's commentsThe author makes a good case for the use of likelihood ratios in presenting evidence. The author cites Nichols and Balding (1991) for the match probability involvingF _ST , and readers will also need to consult Balding and Nichols (1994 and this volume) and Weir (1994). In light of current concern over laboratory errors or fraud, the author's comment that Undetected and unsuspected human error or mischief is potentially a problem in almost all criminal cases, yet no convictions could follow if this possibility was consistently deemed to lead to reasonable doubt is well taken.