A new experimental system for study on adaptive mutations

A super-repressed mutant of purR (purR^S), which encodes a repressor protein controlling expression of purine biosynthetic genes inSalmonella typhimurium, grew very slowly on NCE medium with 10 μg/mL Ade and lactose as sole carbon source (cannot form colonies). However, a phenomenon of late-arising mutations was observed when purR^S mutants were spread on NCE+lactose plates and subjected to a prolonged non-lethal selection. The reconstruction experiments of revertants showed that the late-arising “lac⁺” mutants are not slow growing mutants. Statistical analysis indicated that the distribution of late-arising mutants is Poisson distribution, showing that reversion occurred after plating. The result of co-transductional analysis preliminarily showed that late-arising mutation occurred at selected genepurR or 16 bp PUR box,cis element of structural genepurD. The above results suggest that the phenomenon of late-arising mutation observed by our system is a result of adaptive mutations which are different from random mutations. This is the first time to extend target genes at which adaptive mutations could occur from structural genes involved in carbon metabolism and amino acid biosynthesis totrans regulatory gene coding repressor protein. Our results have provided not only a new proof for generality of adaptive mutations but also a new system for study on adaptive mutations.     

A new look at adaptive mutations in bacteria

This is a short survey of the adaptive mutation processes that arise in non- or slowly-dividing bacterial cells and includes: (i) bacterial models in which adaptive mutations are studied; (ii) the mutagenic lesions from which these mutations derive; (iii) the influence of DNA repair processes on the spectrum of adaptive mutations. It is proposed that in starved cells, likely as during the MFD phenomenon, lesions in tRNA suppressor genes are preferentially repaired and no suppressor tRNAs are formed as a result of adaptive mutations. Perhaps the most provocative proposal is (iv) a hypothesis that the majority of adaptive mutations are selected in a pre-apoptotic state where the cells are either mutated, selected, and survive, or they die.     

A role for replication repair in the genesis of templated mutations

Replication repair mediates error-free bypass of DNA damage in a series of steps that include regression of the replication fork, primer-terminus switching to use the other daughter strand as an undamaged template, primer extension, primer switching back to its cognate template with the primer terminus now having bypassed the damage, and fork rearrangement to a normal configuration. By both genetic and biochemical criteria, bacteriophage T4 catalyzes replication repair with two alternative sets of proteins, one including the gp32 SSB and the gp41 DNA helicase and the other including the UvsX recombinase. In each pathway, synthesis is conducted by the gp43 DNA polymerase. Here we show that defects in gp32, gp41 or UvsX that impair replication repair also increase mutation rates generally, but especially for templated mutations. Such templated mutations are associated with palindromic or direct repeats that are either perfect or imperfect. Models of templated mutagenesis require that the primer terminus switches to an ectopic template, but one that yields mutations instead of error-free bypass. We suggest that the proteins that conduct replication repair normally direct a blocked primer strand specifically to the other daughter strand with considerable accuracy, but that strand switching becomes promiscuous when these proteins are mutationally impaired, thus promoting templated mutations.     

Establishment of new mutations in changing environments

Understanding adaptation in changing environments is an important topic in evolutionary genetics, especially in the light of climatic and environmental change. In this work, we study one of the most fundamental aspects of the genetics of adaptation in changing environments: the establishment of new beneficial mutations. We use the framework of time-dependent branching processes to derive simple approximations for the establishment probability of new mutations assuming that temporal changes in the offspring distribution are small. This approach allows us to generalize Haldane's classic result for the fixation probability in a constant environment to arbitrary patterns of temporal change in selection coefficients. Under weak selection, the only aspect of temporal variation that enters the probability of establishment is a weighted average of selection coefficients. These weights quantify how much earlier generations contribute to determining the establishment probability compared to later generations. We apply our results to several biologically interesting cases such as selection coefficients that change in consistent, periodic, and random ways and to changing population sizes. Comparison with exact results shows that the approximation is very accurate.     

Rapid evolution of adaptive niche construction in experimental microbial populations

Many species engage in adaptive niche construction: modification of the local environment that increases the modifying organism's competitive fitness. Adaptive niche construction provides an alternative pathway to higher fitness, shaping the environment rather than conforming to it. Yet, experimental evidence for the evolutionary emergence of adaptive niche construction is lacking, leaving its role in evolution uncertain. Here we report a direct observation of the de novo evolution of adaptive niche construction in populations of the bacteria Pseudomonas fluorescens. In a laboratory experiment, we allowed several bacterial populations to adapt to a novel environment and assessed whether niche construction evolved over time. We found that adaptive niche construction emerged rapidly, within approximately 100 generations, and became ubiquitous after approximately 400 generations. The large fitness effect of this niche construction was dominated by the low fitness of evolved strains in the ancestrally modified environment: evolved niche constructors were highly dependent on their specific environmental modifications. Populations were subjected to frequent resetting of environmental conditions and severe reduction of spatial habitat structure, both of which are thought to make adaptive niche construction difficult to evolve. Our finding that adaptive niche construction nevertheless evolved repeatably suggests that it may play a more important role in evolution than generally thought.     

Model and test in a fungus of the probability that beneficial mutations survive drift

Determining the probability of fixation of beneficial mutations is critically important for building predictive models of adaptive evolution. Despite considerable theoretical work, models of fixation probability have stood untested for nearly a century. However, recent advances in experimental and theoretical techniques permit the development of models with testable predictions. We developed a new model for the probability of surviving genetic drift, a major component of fixation probability, for novel beneficial mutations in the fungus Aspergillus nidulans, based on the life-history characteristics of its colony growth on a solid surface. We tested the model by measuring the probability of surviving drift in 11 adapted strains introduced into wild-type populations of different densities. We found that the probability of surviving drift increased with mutant invasion fitness, and decreased with wild-type density, as expected. The model accurately predicted the survival probability for the majority of mutants, yielding one of the first direct tests of the extinction probability of beneficial mutations.     

Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host

The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana—tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host''s susceptibility and virus diversity. We have recently shown that TEV populations evolving in A. thaliana ecotypes that differ in susceptibility to infection gained within-host fitness, virulence and infectivity in a manner compatible with a gene-for-gene model of host–parasite interactions: hard-to-infect ecotypes were infected by generalist viruses, whereas easy-to-infect ecotypes were infected by every virus. We characterized the genomes of the evolved viruses and found cases of host-driven convergent mutations. To gain further insights in the mechanistic basis of this gene-for-gene model, we have generated all viral mutations individually as well as in specific combinations and tested their within-host fitness effects across ecotypes. Most of these mutations were deleterious or neutral in their local ecotype and only a very reduced number had a host-specific beneficial effect. We conclude that most of the mutations fixed during the evolution experiment were so by drift or by selective sweeps along with the selected driver mutation. In addition, we evaluated the ruggedness of the underlying adaptive fitness landscape and found that mutational effects were mostly multiplicative, with few cases of significant epistasis.     

Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families

Correlated mutations have been repeatedly exploited for intramolecular contact map prediction. Over the last decade these efforts yielded several methods for measuring correlated mutations. Nevertheless, the application of correlated mutations for the prediction of intermolecular interactions has not yet been explored. This gap is due to several obstacles, such as 3D complexes availability, paralog discrimination, and the availability of sequence pairs that are required for inter- but not intramolecular analyses. Here we selected for analysis fusion protein families that bypass some of these obstacles. We find that several correlated mutation measurements yield reasonable accuracy for intramolecular contact map prediction on the fusion dataset. However, the accuracy level drops sharply in intermolecular contacts prediction. This drop in accuracy does not occur always. In the Cohesin-Dockerin family, reasonable accuracy is achieved in the prediction of both intra- and intermolecular contacts. The Cohesin-Dockerin family is well suited for correlated mutation analysis. Because, however, this family constitutes a special case (it has radical mutations, has domain repeats, within each species each Dockerin domain interacts with each Cohesin domain, see below), the successful prediction in this family does not point to a general potential in using correlated mutations for predicting intermolecular contacts. Overall, the results of our study indicate that current methodologies of correlated mutations analysis are not suitable for large-scale intermolecular contact prediction, and thus cannot assist in docking. With current measurements, sequence availability, sequence annotations, and underdeveloped sequence pairing methods, correlated mutations can yield reasonable accuracy only for a handful of families.     

Human aging and somatic point mutations in mtDNA: A comparative study of generational differences (grandparents and grandchildren)

The accumulation of somatic mutations in mtDNA is correlated with aging. In this work, we sought to identify somatic mutations in the HVS-1 region (D-loop) of mtDNA that might be associated with aging. For this, we compared 31 grandmothers (mean age: 63 ± 2.3 years) and their 62 grandchildren (mean age: 15 ± 4.1 years), the offspring of their daughters. Direct DNA sequencing showed that mutations absent in the grandchildren were detected in a presumably homoplasmic state in three grandmothers and in a heteroplasmic state in an additional 13 grandmothers; no mutations were detected in the remaining 15 grandmothers. However, cloning followed by DNA sequencing in 12 grandmothers confirmed homoplasia in only one of the three mutations previously considered to be homoplasmic and did not confirm heteroplasmy in three out of nine grandmothers found to be heteroplasmic by direct sequencing. Thus, of 12 grandmothers in whom mtDNA was analyzed by cloning, eight were heteroplasmic for mutations not detected in their grandchildren. In this study, the use of genetically related subjects allowed us to demonstrate the occurrence of age-related (> 60 years old) mutations (homoplasia and heteroplasmy). It is possible that both of these situations (homoplasia and heteroplasmy) were a long-term consequence of mitochondrial oxidative phosphorylation that can lead to the accumulation of mtDNA mutations throughout life.     

Disgust as an adaptive system for disease avoidance behaviour

Disgust is an evolved psychological system for protecting organisms from infection through disease avoidant behaviour. This 'behavioural immune system', present in a diverse array of species, exhibits universal features that orchestrate hygienic behaviour in response to cues of risk of contact with pathogens. However, disgust is also a dynamic adaptive system. Individuals show variation in pathogen avoidance associated with psychological traits like having a neurotic personality, as well as a consequence of being in certain physiological states such as pregnancy or infancy. Three specialized learning mechanisms modify the disgust response: the Garcia effect, evaluative conditioning and the law of contagion. Hygiene behaviour is influenced at the group level through social learning heuristics such as 'copy the frequent'. Finally, group hygiene is extended symbolically to cultural rules about purity and pollution, which create social separations and are enforced as manners. Cooperative hygiene endeavours such as sanitation also reduce pathogen prevalence. Our model allows us to integrate perspectives from psychology, ecology and cultural evolution with those of epidemiology and anthropology. Understanding the nature of disease avoidance psychology at all levels of human organization can inform the design of programmes to improve public health.     

Wax synthesis in Brassica oleracea as modified by trichloroacetic acid and glossy mutations

Two different mutations in Brassica oleracea, gl₅ and gl₄ have been re-investigated using acetate-1-¹⁴C labelling in an attempt to define more closely the nature of the genetic blocks to wax synthesis. It has been found that gl₅ is a mutation which blocks elongation in the Step C₂₈–C₃₀. The mutation gl₄ exhibits no elongation block and could be blocked in the decarboxylation Step C₃₀–C₂₉. 0·1 mM TCA supplied in the culture solution of cauliflower seedlings affected the leaf surface by producing a glossy appearance similar to that induced by gl₃ and gl₄. At this concentration growth was not inhibited and the appearance of the plants was normal except for the surface wax. The amount of surface wax produced was about 40% of that in untreated seedlings on a leaf area basis. Slight, but significant changes in wax composition were noted, mainly involving a reduction in C₃₀ acids and aldehydes, a slight reduction (33–29%) in alkane content, and a marked difference in chain length composition of the alkanes with C₂₇ increased relative to C₂₉. Over a range of concentrations from 0·1–1 mM, TCA inhibited incorporation of label from acetate-1-¹⁴C into C₃₀ acids and aldehydes more than into C₂₈ at concentrations 0·4–0·8 mM while label tended to accumulate in C₂₄ and C₂₆ acids; thus elongation C₂₈–C₃₀ was especially sensitive to TCA. TCA also inhibited incorporation into primary alcohols and esters almost as much as into C₂₉ compounds. In spite of relatively specific effects on incorporation of label into longer chain lengths, the resulting block to C₃₀ synthesis is not sufficient to make much difference to the overall rate of C₂₉ synthesis. Both results of analysis of wax from whole plants and experiments with tissue slices in vitro indicated that the effect of TCA in reducing the glaucousness of the leaf surface is a combination of overall reduction of wax synthesis together with slight but significant changes in wax composition.     

基于保护地役权的自然保护地适应性管理方法探讨: 以钱江源国家公园体制试点区为例

我国的自然保护地普遍存在着科学管控难、统一管理难和资金供给难等问题, 即便是国家公园体制试点区也不例外。本文以钱江源国家公园体制试点区为例, 设计了基于细化保护需求的保护地役权制度, 以探索一种能解决上述问题并能体现生态补偿的适应性管理方法, 包括: 细化主要保护对象的管理需求, 结合土地利用类型, 确定实施保护地役权的空间范围; 辨析保护需求和原住民生产、生活之间的关系, 形成正负行为的准则并以行为清单的形式体现; 从生态系统监测指标改善情况、正负行为遵守情况和社区能力建设三个维度制定地役权制度的评价方法; 据此形成地役权合同, 明确供役地人和需役地人的权责利, 形成考虑保护绩效的生态补偿方案。这种方法可以解决自然保护地因为权属不一致造成的生态系统和景观破碎化问题, 缓解社区发展和生态保护之间的矛盾, 在我国南方集体林地占比较高的自然保护地具有适用性。     

A new mechanism for recurrent adaptive radiations

Models of adaptive radiation through intraspecific competition have attracted mounting attention. Here we show how extending such models in a simple manner, by including a quantitative trait under weak directional selection, naturally leads to rich macroevolutionary patterns involving recurrent adaptive radiations and extinctions. Extensive tests demonstrate the robustness of this finding to a wide range of variations in model assumptions. In particular, recurrent adaptive radiations and extinctions readily unfold both for asexual and for sexual populations. Since the mechanisms driving the investigated processes of endogenous diversification result from generic geometric features of the underlying fitness landscapes--frequency-dependent disruptive selection in one trait and weak directional selection in another--the reported phenomena can be expected to occur in a wide variety of eco-evolutionary settings.     

A method for rapid mapping of mutations by plasmid rescue strategy inSaccharomyces cerevisiae

The products ofPRP17 andPRP18 genes are required for the second step of pre-mRNA splicing reactions inSaccharomyces cerevisiae. Temperature-sensitive mutants at either of these loci accumulate products of the first splicing reaction at nonpermissive temperature. To characterize functional regions in these proteins the mutations in three temperature-sensitive alleles ofPRP17 and two temperature-sensitive alleles ofPRP18 were mapped by the plasmid rescue strategy, One of the procedures adopted in the past is plasmid rescue of the mutant allele followed by sequencing of the entire gene. In this work we describe an adaptation of the above procedure that allows, first, rapid mapping of chromosomal segments bearing the mutations, followed by sequence characterization of the minimal segment. The strategy adopted was to integrate a wild-type copy of the gene at the homologous mutant chromosomal locus, followed by recovery of the chromosomal fragments from these integrants as plasmids inE. coli. The recovered plasmids were screened by a complementation assay for those that contained in them the chromosomal mutation. The mutations in all the three alleles ofPRP17 map to a small region in the N-terminal half of the protein, whereas the temperature-sensitive mutations in the two alleles ofPRP18 map to different regions of the PRP18 protein. The recovered mutant plasmids from all five alleles at the two loci were sequenced and the nucleotide changes were found to result in missense mutations in each case. Our strategy is therefore a rapid method to map chromosomal mutations and is of general use in structure-function analysis of cloned genes.     

A new experimental model to study oxygen toxicity

An experimental model was developed in order to study the protective effect of antioxidant molecules. Human diploid WI-38 fibroblasts were cultivated under 2 atm of 95% O2. Antioxidants like alpha-tocopherol or superoxide dismutase (SOD) were added respectively in the culture medium or directly inside the cell through a microinjection technique. With both antioxidant molecules a protection was observed. In the control experiment, cells died within 6 or 8 days depending on the confluency and the malonaldehyde content increased sharply. This model represents a new tool in order to test other antioxidant systems towards an oxidative stress.     

Single-locus tests of microsatellite evolution: multi-step mutations and constraints on allele size

We evaluate some common simulation procedures as well as a recently developed likelihood method used for testing hypotheses regarding microsatellite evolution. Results from simulated data revealed that the tests for the detection of multi-step mutations in general have some power, whereas tests for the presence of constraints on the repeat number have only very limited power. The tests were applied to population data obtained from nine different baleen whale populations. High agreement was found between results obtained using the simulation-based approach and results obtained using a likelihood ratio test. In four of the nine population samples the tests rejected the one-step mutation model. In two instances the significant deviation was due to excess of heterozygosity and in two instances to a reduced level of heterozygosity relative to the expectations under the stepwise mutation model. The former significant deviation was consistent with occasional multi-step mutations, whereas the latter may indicate the presence of constraints on the number of repeats.     

Effects of several meiotic mutations on female meiosis in maize

A modified enzyme digestion technique of ovary isolation followed by staining and squash preparation has allowed us to observe female meiosis in normal maize meiotically dividing megaspore mother cells (MMCs). The first meiotic division in megasporogenesis of maize is not distinguishable from that in mi-crosporogenesis. The second female meiotic division is characterized as follows: (1) the two products of the first meiotic division do not simultaneously enter into the second meiotic division; as a rule, the chalazal-most cell enters division earlier than the micropylar one, (2) often the second of the two products does not proceed with meiosis, but degenerates, and (3) only a single haploid meiotic product of the tetrad remains alive, and this cell proceeds with three rounds of mitoses without any intervening cell wall formation to produce the eight-nucleate embryo sac. This technique has allowed us to study the effects of five meiotic mutations (aml, aml-pral, afdl, dsy *-9101, and dvl) on female meiosis in maize. The effects of the two alleles of the aml gene (aml and aml-pral) and of the afdl and dsy *-9101mutations are the same in both male and female meiosis. The aml allele prevents the entrance of MMCs into meiosis and meiosis is replaced by mitosis; the aml-pral permits MMCs to enter into meiosis, but their progress is stopped at early prophase I stages. The afdl gene is responsible for substitution of the first meiotic (reductional) division by an equational division including the segregation of sister chromatid centromeres at anaphase I. The dsy * -9101 gene exhibits abnormal chromosome pairing; paired homologous chromosomes are visible at pachytene, but only univalents are observed at diakinesis and metaphase I stages. These mutation specific patterns of abnormal meiosis are responsible for the bisexual sterility of these meiotic mutants. The abnormal divergent shape of the spindle apparatus and the resulting abnormal segregation of homologous chromosomes observed in micro-sporogenesis in plants homozygous for the dv1 mutation have not been found in meiosis of megasporogenesis. Only male sterility is induced by the dv1 gene in the homozygous condition. © 1993 Wiley-Liss, Inc.     

Understanding leukemic hematopoiesis as a complex adaptive system

Normal and abnormal hematopoiesis is working as a complex adaptive system. From this perspective, the development and the behavior of hematopoietic cell lineages appear as a balance between normal and abnormal hematopoiesis in the setting of a functioning or malfunctioning microenvironment under the control of the immune system and the influence of hereditary and environmental events.