Unstable DNA Repair Genes Shaped by Their Own Sequence Modifying Phenotypes

The question of whether natural selection favors genetic stability or genetic variability is a fundamental problem in evolutionary biology. Bioinformatic analyses demonstrate that selection favors genetic stability by avoiding unstable nucleotide sequences in protein encoding DNA. Yet, such unstable sequences are maintained in several DNA repair genes, thereby promoting breakdown of repair and destabilizing the genome. Several studies have therefore argued that selection favors genetic variability at the expense of stability. Here we propose a new evolutionary mechanism, with supporting bioinformatic evidence, that resolves this paradox. Combining the concepts of gene-dependent mutation biases and meiotic recombination, we argue that unstable sequences in the DNA mismatch repair (MMR) genes are maintained by their own phenotype. In particular, we predict that human MMR maintains an overrepresentation of mononucleotide repeats (monorepeats) within and around the MMR genes. In support of this hypothesis, we report a 31% excess in monorepeats in 250 kb regions surrounding the seven MMR genes compared to all other RefSeq genes (1.75 vs. 1.34%, P = 0.0047), with a particularly high content in PMS2 (2.41%, P = 0.0047) and MSH6 (2.07%, P = 0.043). Based on a mathematical model of monorepeat frequency, we argue that the proposed mechanism may suffice to explain the observed excess of repeats around MMR genes. Our findings thus indicate that unstable sequences in MMR genes are maintained through evolution by the MMR mechanism. The evolutionary paradox of genetically unstable DNA repair genes may thus be explained by an equilibrium in which the phenotype acts back on its own genotype.     

GENE FLOW FROM DOMESTICATED SPECIES TO WILD RELATIVES: MIGRATION LOAD IN A MODEL OF MULTIVARIATE SELECTION

Domesticated species frequently spread their genes into populations of wild relatives through interbreeding. The domestication process often involves artificial selection for economically desirable traits. This can lead to an indirect response in unknown correlated traits and a reduction in fitness of domesticated individuals in the wild. Previous models for the effect of gene flow from domesticated species to wild relatives have assumed that evolution occurs in one dimension. Here, I develop a quantitative genetic model for the balance between migration and multivariate stabilizing selection. Different forms of correlational selection consistent with a given observed ratio between average fitness of domesticated and wild individuals offsets the phenotypic means at migration–selection balance away from predictions based on simpler one-dimensional models. For almost all parameter values, correlational selection leads to a reduction in the migration load. For ridge selection, this reduction arises because the distance the immigrants deviates from the local optimum in effect is reduced. For realistic parameter values, however, the effect of correlational selection on the load is small, suggesting that simpler one-dimensional models may still be adequate in terms of predicting mean population fitness and viability.     

The importance of hardening and winter temperature for growth in mountain birch populations

Seedlings of five mountain birch populations (Betula pubescens Ehrh. ssp. czerepanovii) from Fennoscandia and Iceland were raised and grown at natural daylengths at Tromsø, Norway (69°N) and different temperatures during late summer and fall season, followed by winter temperature treatment at ambient and +4 °C above ambient temperatures at Bergen, Norway (60°N). The experiment took place during two seasons (2000/01 and 2001/02). The following summer shoot and biomass growth were reduced as a result of winter warming and subsequent premature dehardening in early flushing provenances and treatments. Biomass increased in plants grown at low hardening temperature when compared with high temperature treatment. As a conclusion, increased winter temperatures would tend to increase the risk of spring frost damage and reduce growth in birch seedlings, because the differences between the frost hardening and ambient temperatures are decreasing, and because the time from budbreak to dehardening is shortened. The results are discussed in relation to simultaneous experiments with frost hardiness in the same populations and treatments.     

Agar culture of Piscirickettsia salmonis, a serious pathogen of farmed salmonid and marine fish

Piscirickettsia salmonis, a serious bacterial pathogen of farmed marine fish, previously considered culturable only in eukaryotic cell-culture systems, was grown for the first time on agar and broth containing enhanced levels of cysteine, thus greatly increasing the potential for isolation, in vitro culture and study of this organism. Virulence towards Atlantic salmon following passage on agar media was retained in a controlled laboratory trial. Of the studied temperatures, optimal growth on agar was observed at 22 degrees C.     

Survey of Genomic Diversity among Enterococcus faecalis Strains by Microarray-Based Comparative Genomic Hybridization

We have compared nine Enterococcus faecalis strains with E. faecalis V583 by comparative genomic hybridization using microarrays (CGH). The strains used in this study (the “test” strains) originated from various environments. CGH is a powerful and promising tool for obtaining novel information on genome diversity in bacteria. By CGH, one obtains clues about which genes are present or divergent in the strains, compared to a reference strain (here, V583). The information obtained by CGH is important from both ecological and systematic points of view. CGH of E. faecalis showed considerable diversity in gene content: Compared to V583, the percentage of divergent genes in the test strains varied from 15% to 23%, and 154 genes were divergent in all strains. The main variation was found in regions corresponding to exogenously acquired or mobile DNA in V583. Antibiotic resistance genes, virulence factors, and integrated plasmid genes dominated among the divergent genes. The strains examined showed various contents of genes corresponding to the pTEF1, pTEF2, and pTEF3 genes in V583. The extensive transport and metabolic capabilities of V583 appeared similar in the test strains; CGH indicated that the ability to transport and metabolize various carbohydrates was similar in the test strains (verified by API 50 CH assays). The contents of genes related to stress tolerance appeared similar in V583 and the nine test strains, supporting the view of E. faecalis as an organism able to resist harsh conditions.     

Regioselective metabolism of phenanthrene in Atlantic cod (Gadus morhua): studies on the effects of monooxygenase inducers and role of cytochromes P-450

The polycyclic aromatic hydrocarbon phenanthrene was converted mainly (>90%) to the 1,2-dihydrodiol when metabolized in vivo by the marine teleost cod. This is also found in other bony fishes, but contrary to what is known from cartilaginous fish, crustaceans and mammals, where the K-region 9,10-dihydrodiol is the main metabolite. When liver microsomal preparations from differently pretreated cod were incubated with phenanthrene in vitro, the metabolic profile was dramatically different from the in vivo pattern, as shown by gas chromatography—mass spectrometry. The microsomes from untreated, phenanthrene, phenobarbital and pregnenolone-16-carbonitrile-treated cod converted phenanthrene mainly, but to a varying extent, to the 9,10-dihydrodiol. Treatment with β-naphthoflavone (BNF), however, resulted in a large increase in the oxidation at the 1,2-position, along with a four- to seven-fold increase in specific activity. The major cytochrome P-450 isozyme purified from BNF-treated cod liver (P-450c) showed highest activity with phenanthrene (a turnover of 0.18 nmol/min per nmol P-450), but with about equal selectivity for the 1,2- and 9,10-region of the substrate in a reconstituted system with phospholipid and NADPH-cytochrome P-450 reductase. The low regioselectivity was also observed as a lack of regioselective inhibition of microsomal phenanthrene metabolism with antiserum to cod P-450c. Two of the minor isozymes, cod cytochromes P-450b and d, showed a similar turnover to P-450c, but with a stronger selectivity for the 1,2-position (55–60%). The results indicate that other control systems, in addition to the content of individual P-450-forms in the regulatory systems, in addition to the content of individual P-450-forms in the endoplasmic reticulum, are involved in the in vivo transformation of phenanthrene by cod to the 1,2-dihydrodiol metabolite.     

Circadian-Stage Dependence of Methotrexate In A Keratinized Epithelium. an in-vivo Study Using Flow Cytometry On the Hamster Cheek Pouch Epithelium

The partially synchronized cell system of the hamster cheek pouch epithelium shows a characteristic diurnal rhythm of cell proliferation. Bolus injections of methotrexate (Mtx) in both lethal (10 g/m²) and non-lethal (2 g/m²) doses were found to inhibit cell-cycle progression primarily by impairing the G₁/S transition. the results were obtained by flow cytometric DNA analysis. the inhibitory effect of Mtx manifested itself as a relative decrease of the S fraction (drug-effector phase), and was found to be dependent both on the dose and on the time of the day it was given. A bolus injection of Mtx was given either at 1200 hr (when a minimal number of cells are in S phase) or at 0200 hr (when a maximum number of cells are in S phase). the greatest cumulative decrease in S fraction was seen when the injection was given at 1200 hr. the time between injection and the effect (seen as a decrease in S fraction) was independent of the time of the Mtx injection, but seemed instead to be related to the natural diurnal period of increasing flux from G₁ to S phase (at the onset of the dark period). the main effect (the relative decrease in S fraction) was repeated during the following 24-hr period, pointing to a protracted effect of Mtx on G₁ cells. G₁ cells affected by the initial high Mtx plasma concentration seem to be responsible for the reduced influx into S phase in both the first and second 24-hr period. In earlier toxicological studies, the survival rate of hamsters was dependent on the time of injection and was highest after injection at 1200 hr. Thus maximum cytokinetic effect on epithelial cells was found at the time of the day when there was a minimum lethal effect on the animal.     

Survey of genomic diversity among Enterococcus faecalis strains by microarray-based comparative genomic hybridization

We have compared nine Enterococcus faecalis strains with E. faecalis V583 by comparative genomic hybridization using microarrays (CGH). The strains used in this study (the "test" strains) originated from various environments. CGH is a powerful and promising tool for obtaining novel information on genome diversity in bacteria. By CGH, one obtains clues about which genes are present or divergent in the strains, compared to a reference strain (here, V583). The information obtained by CGH is important from both ecological and systematic points of view. CGH of E. faecalis showed considerable diversity in gene content: Compared to V583, the percentage of divergent genes in the test strains varied from 15% to 23%, and 154 genes were divergent in all strains. The main variation was found in regions corresponding to exogenously acquired or mobile DNA in V583. Antibiotic resistance genes, virulence factors, and integrated plasmid genes dominated among the divergent genes. The strains examined showed various contents of genes corresponding to the pTEF1, pTEF2, and pTEF3 genes in V583. The extensive transport and metabolic capabilities of V583 appeared similar in the test strains; CGH indicated that the ability to transport and metabolize various carbohydrates was similar in the test strains (verified by API 50 CH assays). The contents of genes related to stress tolerance appeared similar in V583 and the nine test strains, supporting the view of E. faecalis as an organism able to resist harsh conditions.     

Arctic browning: Impacts of extreme climatic events on heathland ecosystem CO2 fluxes

Extreme climatic events are among the drivers of recent declines in plant biomass and productivity observed across Arctic ecosystems, known as “Arctic browning.” These events can cause landscape‐scale vegetation damage and so are likely to have major impacts on ecosystem CO₂ balance. However, there is little understanding of the impacts on CO₂ fluxes, especially across the growing season. Furthermore, while widespread shoot mortality is commonly observed with browning events, recent observations show that shoot stress responses are also common, and manifest as high levels of persistent anthocyanin pigmentation. Whether or how this response impacts ecosystem CO₂ fluxes is not known. To address these research needs, a growing season assessment of browning impacts following frost drought and extreme winter warming (both extreme climatic events) on the key ecosystem CO₂ fluxes Net Ecosystem Exchange (NEE), Gross Primary Productivity (GPP), ecosystem respiration (R_eco) and soil respiration (R_soil) was carried out in widespread sub‐Arctic dwarf shrub heathland, incorporating both mortality and stress responses. Browning (mortality and stress responses combined) caused considerable site‐level reductions in GPP and NEE (of up to 44%), with greatest impacts occurring at early and late season. Furthermore, impacts on CO₂ fluxes associated with stress often equalled or exceeded those resulting from vegetation mortality. This demonstrates that extreme events can have major impacts on ecosystem CO₂ balance, considerably reducing the carbon sink capacity of the ecosystem, even where vegetation is not killed. Structural Equation Modelling and additional measurements, including decomposition rates and leaf respiration, provided further insight into mechanisms underlying impacts of mortality and stress on CO₂ fluxes. The scale of reductions in ecosystem CO₂ uptake highlights the need for a process‐based understanding of Arctic browning in order to predict how vegetation and CO₂ balance will respond to continuing climate change.