Evolution of robustness in digital organisms

We study the evolution of robustness in digital organisms adapting to a high mutation rate. As genomes adjust to the harsh mutational environment, the mean effect of single mutations decreases, up until the point where a sizable fraction (up to 30% in many cases) of the mutations are neutral. We correlate the changes in robustness along the line of descent to changes in directional epistasis, and find that increased robustness is achieved by moving from antagonistic epistasis between mutations towards codes where mutations are, on average, independent. We interpret this recoding as a breakup of linkage between vital sections of the genome, up to the point where instructions are maximally independent of each other. While such a recoding often requires sacrificing some replication speed, it is the best strategy for withstanding high rates of mutation.     

Evolution of synchronization and desynchronization in digital organisms

We present a study in the evolution of temporal behavior, specifically synchronization and desynchronization, through digital evolution and group selection. In digital evolution, a population of self-replicating computer programs exists in a user-defined computational environment and is subject to instruction-level mutations and natural selection. Group selection links the survival of the individual to the survival of its group, thus encouraging cooperation. Previous approaches to engineering synchronization and desynchronization algorithms have taken inspiration from nature: In the well-known firefly model, the only form of communication between agents is in the form of flash messages among neighbors. Here we demonstrate that populations of digital organisms, provided with a similar mechanism and minimal information about their environment, are capable of evolving algorithms for synchronization and desynchronization, and that the evolved behaviors are robust to message loss. We further describe how the evolved behavior for synchronization mimics that of the well-known Ermentrout model for firefly synchronization in biology. In addition to discovering self-organizing behaviors for distributed computing systems, this result indicates that digital evolution may be used to further our understanding of synchronization in biology.     

Evolution of resistance to quorum quenching in digital organisms

Quorum sensing (QS) is a collective behavior whereby actions of individuals depend on the density of the surrounding population. Bacteria use QS to trigger secretion of digestive enzymes, formation and destruction of biofilms, and, in the case of pathogenic organisms, expression of virulence factors that cause disease. Investigations of mechanisms that prevent or disrupt QS, referred to as quorum quenching, are of interest because they provide a new alternative to antibiotics for treating bacterial infections. Traditional antibiotics either kill bacteria or inhibit their growth, producing selective pressures that promote resistant strains. In contrast, quorum quenching and other so-called anti-infective strategies focus on altering behavior. In this article we evolve QS in populations of digital organisms, a type of self-replicating computer program, and investigate the effects of quorum quenching on these populations. Specifically, we injected the populations with mutant organisms that were impaired in selected ways to disrupt the QS process. The experimental results indicate that the rate at which these mutants are introduced into a population influences both the evolvability of QS and the persistence of an existing QS behavior. Surprisingly, we also observed resistance to quorum quenching. Effectively, populations evolved resistance by reaching quorum at lower cell densities than did the parent strain. Moreover, the level of resistance was highest when the rate of mutant introduction increased over time. These results show that digital organisms can serve as a model to study the evolution and disruption of QS, potentially informing wet-lab studies aimed at identifying targets for anti-infective development.     

Alpha-tropomyosin mutually exclusive exon selection: competition between branchpoint/polypyrimidine tracts determines default exon choice

We have used exons 2 and 3 of the rat alpha-tropomyosin gene to analyze the basis of mutually exclusive exon selection. The basis of the strict mutually exclusive behavior of this exon pair is enforced by the proximity of the exon 3 branchpoint to the 5' splice site of exon 2. With the exception of smooth muscle cells, exon 3 rather than exon 2 is incorporated into mRNA in all cell types. We show here, using both in vivo and in vitro cell-free systems, that this alternative exon selection is a consequence of general principles that govern 3' splice site selection. In the absence of exon 3, exon 2 is utilized efficiently in all cells. Selection of exon 3 is therefore the default result of a competition between exons 2 and 3 for the flanking constitutive splice sites. The basis of this competition is the relative strength of the polypyrimidine tract/branchpoint elements of the two exons. The major determinant of this splice site strength is the pyrimidine content adjacent to the branchpoint, and this involves no other sequence specificity. The branchpoint elements play an important but secondary role. The functional strengths of the different polypyrimidine tract/branchpoint combinations, as determined in cis competition assays, showed a perfect correlation with their binding affinities to a spliceosome component that interacts with the pre-mRNA in an ATP-independent manner. Selection of exon 3 in most cell types therefore reflects the preferential interaction of these splice site elements with constitutive splicing factors early in spliceosome assembly. The aspects of splice site selection analyzed here are likely to be of general applicability to constitutive and alternative pre-mRNA splicing.     

Modalities of aging in organisms with different strategies of resource allocation

Although the progress of aging research relies heavily on a theoretical framework, today there is no consensus on many critical questions in aging biology. I hypothesize that a systematic analysis of the intersection of different evolutionary mechanisms of aging with diverse resource allocation strategies in different organisms may reconcile aging hypotheses. The application of disposable soma, mutation accumulation, antagonistic pleiotropy, and life-history theory is considered across organisms with asexual reproduction, organisms with sexual reproduction and indeterminate growth in different conditions of extrinsic mortality, and organisms with determinate growth, with endotherms/homeotherms as a subgroup. This review demonstrates that different aging mechanisms are complementary to each other, and in organisms with different resource allocation strategies they form aging modalities ranging from immortality to suicidal programs. It also revamps the role of growth arrest in aging. Growth arrest evolved in many different groups of organisms as a result of resource reallocation from growth to reproduction (e.g., semelparous animals, holometabolic insects), or from growth to nutrient storage (endotherms/homeotherms). Growth arrest in different animal lineages has similar molecular mechanisms and similar consequences for longevity due to the conflict between growth-promoting and growth-suppressing programs and suppression of regenerative capacity.     

The emergence of overlapping scale-free genetic architecture in digital organisms

We have studied the evolution of genetic architecture in digital organisms and found that the gene overlap follows a scale-free distribution, which is commonly found in metabolic networks of many organisms. Our results show that the slope of the scale-free distribution depends on the mutation rate and that the gene development is driven by expansion of already existing genes, which is in direct correspondence to the preferential growth algorithm that gives rise to scale-free networks. To further validate our results we have constructed a simple model of gene development, which recapitulates the results from the evolutionary process and shows that the mutation rate affects the tendency of genes to cluster. In addition we could relate the slope of the scale-free distribution to the genetic complexity of the organisms and show that a high mutation rate gives rise to a more complex genetic architecture.     

Serological cross-reactivity between different Chlamydia-like organisms

The serological cross-reactivity between different recently described Chlamydia-related organisms was determined. Mouse sera exhibited a strong reactivity against autologous antigen and closely related heterologous antigen but no cross-reactivity with distantly related species. These results are important to better interpret serological studies and assess the pathogenic role of these obligate intracellular bacteria.     

数字化进程中医院图书馆信息资源建设及共享方案

数字图书馆是当今图书馆事业的发展方向,信息资源建设则是数字图书馆建设的核心内容之一。本文分析了在数字化进程中医院图书馆的藏书特点以及信息资源构成,提出了数字化进程中医院图书馆信息资源共享方案。     

Antigenic competition in vitro between heterologous erythrocytes

The phenomenon of antigenic competition between different heterologous red cells has been studied in vitro using the Mishell-Dutton technique of cultivating mouse spleen cells. If spleen cells from animals heavily pre-immunized in vivo against one antigen are cultured together with this antigen and a second antigen, the antibody response against the second antigen is depressed. The number of antigen sensitive cells was found to be normal during antigenic competition. Competition is transferrable from one population of lymphoid cells to another. Thus, heavily preimmunized cells cultivated in the presence of normal cells suppressed the antibody response of the latter. However, no soluble mediator of this suppression could be recovered from media of cultures displaying antigenic competition or from the serum of animals the spleens of which showed antigenic competition in vitro. A thymus-independent antigen could not give rise to antigenic competition, but the response to such an antigen was subjected to competition. The finding suggests that intensive specific stimulation of lymphoid cells under thymic influence causes expression of antigenic competition. The phenomenon could either be due to a production of inhibitory factors active over a short distance, only, or to a direct inhibitory cell-to-cell interaction between antigen-activated cells and precursor cells for antibody production.     

Studies on the mechanism of antigenic competition: analysis of competition between synthetic polypeptide antigens

Antigenic competition has been studied in C3H/HeJ mice between determinants of the multichain synthetic polypeptide antigens, (Phe, G)-A–L, (T, G)-Pro–L and (Phe, G)-Pro–L. Since these mice did not respond detectably to (T, G) and only very weakly to A–L, the relevant immunopotent regions involved were Pro – L and (Phe, G). Thus, these animals generated a good response to the (Phe, G) determinant, when given as (Phe, G)-A–L, and a good response to Pro – L, when administered either as such or as (T, G)-Pro–L. However, when the immunogen was (Phe, G)-Pro–L, the antibody response was mainly towards Pro–L, whereas a very poor response was obtained to the (Phe, G) specificity. This is interpreted as antigenic competition between Pro–L and (Phe, G), with Pro–L the dominant and (Phe, G) the suppressed determinant. Competition was also demonstrated with mixtures of (T, G)-Pro–L and (Phe, G)-A–L. Competition with the mixed antigens was dependent on the relative amounts of the immunogens in the mixtures. Thus, a molar excess of (T, G)-Pro–L over (Phe, G)-A–L of 5 to 1 suppressed the response to (Phe, G), but an excess of (Phe, G)-A–L of 5 to 1 suppressed the of 25 to 1 caused suppression of the anti-Pro–L response. With equimolar mixtures, an optimal primary response to both (Phe, C) and Pro–L was observed. Where competition had occurred in the primary response, no priming was detected for a secondary response. Under certain conditions immunological memory could be suppressed by competition even though an apparently normal primary response had occurred, suggesting that memory is more susceptible to suppression by competition than is the primary response. The ability of an excess of (Phe, G)-A–L to suppress the response to Pro–L could be reproduced completely with A–L alone. Thus, a molecule that is very poorly immunogenic, but which functions as a carrier for haptens, can be successful in competition.     

Raymond Pearl memorial lecture, 1988: Evolution of mitochondrial DNA in human and other organisms

Within the last ten years complete sequencing of mitochondrial DNA in human and several other species, sequencing of nuclear and mitochondrial ribosomal and transfer RNAs in many species of bacteria, fungi, plants, and animals, and population studies of restriction enzyme polymorphism in the mtDNAs of insects, mammals and sixteen species of primates produced a wide range of new data and theory in molecular evolutionary genetics. These data support the endosymbiotic origin of the eukaryotic cell, the evolution of the Genus Homo with Pan as the closest related living genus, and the origin of modern Homo sapiens by gradualistic, anagenetic, regional phyletic transformation from Homo erectus.     

Malathion influences competition between Aedes albopictus and Aedes japonicus

Competitive interactions may facilitate or repel invaders into new communities, and these interactions may depend on other environmental conditions such as the presence of pesticides. Malathion is widely used in controlling agricultural pests and mosquitoes worldwide. Small amounts of malathion, previously considered inconsequential, may in fact increase in lethality when combined with biotic stressors in aquatic systems. We tested whether low concentrations of malathion (0.11 ppm) that are often detected in aquatic systems, affect competition between two invasive mosquito species Aedes albopictus (Skuse) and Aedes japonicus Theobald. There were no survivors of Ae. japonicus larvae in malathion. There was a significant negative effect of Ae. japonicus density on Ae. albopictus survival, but this effect was absent in the presence of malathion. There was also a moderate negative effect of Ae. japonicus density on Ae. albopictus female size, but this effect was absent in the presence of malathion. These findings indicate that pesticide-mediated alterations in competition and species-specific differences in susceptibility to pesticides could play a role in enhancing invasive potential of Ae. albopictus.     

In-situ competition between protamine and fluorochromes for sperm DNA

In this study we investigated the relationship between the presence of bound protamine on mouse and human sperm DNA and the level of chromomycin A3 (CMA3) and 4'6-diamidino-2-phenylindole (DAPI) fluorescence. This was accomplished by performing a competition assay between salmon protamine and fluorochromes on decondensed spermatozoa that had their nuclear proteins extracted and were fixed on slides. Various concentrations (0, 0.005, 0.0225, 0.05, 0.225, 0.5 and 5 mg/ml) of salmon protamine were added to either the CMA3 or DAPI staining solutions. Fluorescence emission measurements of stained sperm nuclei were then performed using a microfluorometer. When the treated decondensed sperm heads were stained with either CMA3 or DAPI all spermatozoa were found to fluoresce intensely. The addition of protamines to the spermatozoa led to an elimination of CMA3 fluorescence, while the intensity of DAPI staining was decreased to approximately 50% at the highest concentrations of protamine. The addition of increasing amounts of salmon protamine also induced the sperm nuclei to regain their initial condensed appearance. This study shows that protamine retains a strong affinity for sperm DNA in situ and that CMA3 fluorescence is a strong indicator of the protamination state of spermatozoa.      

Antigenic competition between heterologous erythrocytes in mice. Immunological and histological studies exploring mechanisms of the antigenic competition.

To explore the mechanisms of antigenic competition, immunological and histological studies were made on mice using non-crossreacting heterologous erythrocyte antigens, i.e. sheep (SRBC), horse (HRBC) and chicken (CRBC) erythrocytes. Deficiency in the competition-inducing capacity of CRBC which we demonstrated in a previous paper was corroborated by the results that under any experimental conditions examined CRBC were unable to induce the competition. Of interest in the studies was that when anti-HRBC antibody responses of mice pre-injected with SRBC, i.e. competing antigen, were examined on day 2 and day 4 of HRBC-immunization, the day-2 response was revealed to be significantly enhanced, whereas the day-4-response was markedly suppressed as a result of the antigenic competition. By contrast, pre-injection with CRBC, i.e. non-competing antigen, did not affect at all either day-2 or day-4 anti-HRBC response of mice. Histological features of the spleens of mice either being prepared for antigenic competition or undergoing competitively suppressed antibody response were characterized by prominent regeneration of hyperplastic germinal centres, involving appearance of numerous tingible bodies and distinct collars of small lymphocytes which suggested massive proliferation and degeneration of lymphocytes. The spleens of mice in the immunological state indifferent to antigenic competition were characterized by huge lymphatic follicles which contained very few tingible bodies and were circumscribed by a markedly attenuated zone of small lymphocytes. From all these results, we suggest that massive proliferation and differentiation of T lymphocytes, probably toward regulatory (suppressor) T cells, could account for a mechanism of antigenic competition, and that deficient competition-inducing capacity of CRBC should be ascribed to weakness of their capacity in activation of the regulatory T lymphocytes.     

Correlation between heart rate and performance during Olympic windsurfing competition

The aim of this study was to examine the heart rate (HR) response to Olympic windsurfing competition and to check if there was any correlation between racing HR, performance, and the variables measured during laboratory maximal exercise. Ten elite windsurfers [age: 20.93 (3.46) years; height: 178.10 (6.34) cm; body mass: 66.79 (5.90) kg] performed a laboratory maximal oxygen consumption (VO_2max) trial and national windsurf competitions wearing a HR monitor. One hundred and forty-three individual races were examined. Racing HR was expressed as a percentage of (1) HR_max (maximal treadmill HR) and (2) HR_reserve (HR_max−HR_rest). The performance (racing classification: RC, which is inversely proportional to performance) was significantly correlated to the racing HR response in both light wind (LW): LW−RC=−0.12(%HR_reserve)+13.03; r=−0.71, r ²=0.50, p<0.001, and medium wind (MW): MW−RC=−0.11(%HR_reserve)+10.99; r=−0.66, r ²=0.43, p<0.001. The results showed similar correlations between performance and %HR_max. Post racing lactate concentration was higher in LW compared to MW [7.14 (0.21) and 5.18 (2.02) mmol·l⁻¹, respectively]. There was a negative correlation between the highest racing HR (%HR_reserve) of each athlete and the second ventilatory threshold expressed as a percentage of VO˙_2max (r=–0.71, p<0.05). To summarize, this study showed that light and medium wind Olympic windsurfing performances are highly dependent on the capacity of the athlete to maintain a high HR for long periods of time. Furthermore, windsurfing is highly dependent on the athlete's physical fitness level as shown by the correlations between racing HRs and laboratory physiological variables. Electronic Publication     

Antigenic competition between and endotoxic adjuvant and a protein antigen

Antigenic competition between bovine gamma globulin (BGG) and endotoxin from a smooth strain (S-ET) and a rough (R-ET) heptoseless mutant strain of Salmonella minnesota was studied in mice. Both endotoxins acted as adjuvants for enhancing the antibody response to BGG. However, other work showed that the R-ET had minimal antigenicity, and it was used as a control for the competition studies. Antigenic competition between BGG and endotoxin as expressed by a suppression of the antibody response to BGG could not be demonstrated when varying adjuvant doses of S-ET or R-ET were injected simultaneously with a small constant dose of BGG into normal mice. However, mice presensitized with S-ET several weeks before immunization with the S-ET and BGG combination produced anti-BGG levels which were four to eightfold lower than in normal mice. Nearly complete suppression of the anti-BGG response could be obtained in presensitized mice by reducing the BGG dose 10-fold or by increasing the adjuvant dose of endotoxin. Mice pretreated with R-ET and challenged with BGG plus S-ET or R-ET showed no depression of the anti-BGG response. These and other experiments confirmed the immunological basis of the competitive effect.     

Homeostatic competition between food intake and temperature regulation in rats

Rats obliged to leave a thermoneurtral box to feed at air temperatures (T_a) of 25°, 5 or ?15°C reduced the total time spent feeding and the duration of each meal as T_a fell, but increased their food intake by eating faster. Increasing the palatability of the food offered at ?15°C T_a did not prolong feeding but further increased food intake and the speed of eating. The estimated maximum fall in rectal temperature during feeding at ?15°C was small (0.48°±0.15°C, S.E.) but skin temperatures of ears and tail tip fell to near 0°C. These rats were able to maintain near-normal balances of food intake and body temperature by reallocating the times spent feeding and sheltering and by altering the speed of eating; they thus resolved a conflict between hunger and cold discomfort with little evidence of a strain on homeostasis.