Compensatory evolution for a gene deletion is not limited to its immediate functional network

<p>Abstract</p> <p>Background</p> <p>Genetic disruption of an important phenotype should favor compensatory mutations that restore the phenotype. If the genetic basis of the phenotype is modular, with a network of interacting genes whose functions are specific to that phenotype, compensatory mutations are expected among the genes of the affected network. This perspective was tested in the bacteriophage T3 using a genome deleted of its DNA ligase gene, disrupting DNA metabolism.</p> <p>Results</p> <p>In two replicate, long-term adaptations, phage compensatory evolution accommodated the low ligase level provided by the host without reinventing its own ligase. In both lines, fitness increased substantially but remained well below that of the intact genome. Each line accumulated over a dozen compensating mutations during long-term adaptation, and as expected, many of the compensatory changes were within the DNA metabolism network. However, several compensatory changes were outside the network and defy any role in DNA metabolism or biochemical connection to the disruption. In one line, these extra-network changes were essential to the recovery. The genes experiencing compensatory changes were moderately conserved between T3 and its relative T7 (25% diverged), but the involvement of extra-network changes was greater in T3.</p> <p>Conclusion</p> <p>Compensatory evolution was only partly limited to the known functionally interacting partners of the deleted gene. Thus gene interactions contributing to fitness were more extensive than suggested by the functional properties currently ascribed to the genes. Compensatory evolution offers an easy method of discovering genome interactions among specific elements that does not rest on an a priori knowledge of those elements or their interactions.</p

Oxetane ethers are formed reversibly in the lithium-catalyzed Friedel-Crafts alkylation of phenols with oxetanols: synthesis of dihydrobenzofurans, diaryloxetanes, and oxetane ethers

Studies on the mechanism and intermediate products in the Friedel–Crafts reaction between oxetanols and phenols are presented. Formation of O-alkylated intermediates is identified using 1H NMR spectroscopy, in a reversible formation of the kinetic oxetane ether products. An interesting relationship between the electronic nature of the nucleophile and the degree of O-alkylation is uncovered. For phenols substituted with an electron withdrawing group such as CN, oxetane ethers are the only products isolated regardless of reaction time. Increasing the electron rich nature of the phenol leads to an increased proportion of the thermodynamic C-alkylated Friedel–Crafts products after just one hour and as the sole product/s after extended reaction times. These studies have enabled a more complete catalytic cycle to be proposed. Using the same lithium catalyst and carefully selected reaction times, several examples of oxetane ethers are successfully isolated as novel bioisosteres for ester groups

Uni-modal versus joint segmentation for region-based image fusion

A number of segmentation techniques are compared with regard to their usefulness for region-based image and video fusion. In order to achieve this, a new multi-sensor data set is introduced containing a variety of infra-red, visible and pixel fused images together with manually produced 'ground truth' segmentations. This enables the objective comparison of joint and unimodal segmentation techniques. A clear advantage to using joint segmentation over unimodal segmentation, when dealing with sets of multi-modal images, is shown. The relevance of these results to region-based image fusion is confirmed with task-based analysis and a quantitative comparison of the fused images produced using the various segmentation algorithms

Effect of ammonium fluoride doping on the ice III to ice IX phase transition

Ice III is a hydrogen-disordered phase of ice that is stable between about 0.2 and 0.35 GPa. Upon cooling, it transforms to its hydrogen-ordered counterpart ice IX within the stability region of ice II. Here, the effect of ammonium fluoride doping on this phase transition is investigated, which is followed for the first time with in situ neutron diffraction. The a and c lattice constants are found to expand and contract, respectively, upon hydrogen ordering, yielding an overall negative volume change. Interestingly, the anisotropy in the lattice constants persists when ice IX is fully formed, and negative thermal expansion is observed. Analogous to the isostructural keatite and β-spodumenes, the negative thermal expansion can be explained through the buildup of torsional strain within the a–b plane as the helical “springs” within the structure expand upon heating. The reversibility of the phase transition was demonstrated upon heating. As seen in diffraction and Raman spectroscopy, the ammonium fluoride doping induces additional residual hydrogen disorder in ice IX and is suggested to be a chemical way for the “excitation” of the configurational ice-rules manifold. Compared to ice VIII, the dopant-induced hydrogen disorder in ice IX is smaller, which suggests a higher density of accessible configurational states close to the ground state in ice IX. This study highlights the importance of dopants for exploring the water’s phase diagram and underpins the highly complex solid-state chemistry of ice

Synthesis of oxetane and azetidine ethers as ester isosteres by Brønsted acid catalysed alkylation of alcohols with 3-aryl-oxetanols and 3-aryl-azetidinols

Oxetanes and azetidines continue to draw significant interest in medicinal chemistry, as small, polar and non-planar motifs. Oxetanes also represent interesting surrogates for carbonyl-containing functional groups. Here we report a synthesis of 3,3- disubstituted oxetane- and azetidine-ethers, with comparisons made to the ester functional group. The tertiary benzylic alcohols of the 4-membered rings are selectively activated using Brønsted acid catalysis and reacted with simple alcohols to form the ethers and maintain the oxetane ring intact. This approach avoids the use of strong bases and halide alkylating agents and allows alcohol libraries to be leveraged. Oxetane ethers demonstrate excellent chemical stability across a range of conditions and an improved stability vis-à-vis analogous esters under basic and reducing conditions

The Phenotype-Fitness Map in Experimental Evolution of Phages

Evolutionary biologists commonly interpret adaptations of organisms by reference to a phenotype-fitness map, a model of how different states of a phenotype affect fitness. Notwithstanding the popularity of this approach, it remains difficult to directly test these mappings, both because the map often describes only a small subset of phenotypes contributing to total fitness and because direct measures of fitness are difficult to obtain and compare to the map. Both limitations can be overcome for bacterial viruses (phages) grown in the experimental condition of unlimited hosts. A complete accounting of fitness requires 3 easily measured phenotypes, and total fitness is also directly measurable for arbitrary genotypes. Yet despite the presumed transparency of this system, directly estimated fitnesses often differ from fitnesses calculated from the phenotype-fitness map. This study attempts to resolve these discrepancies, both by developing a more exact analytical phenotype-fitness map and by exploring the empirical foundations of direct fitness estimates. We derive an equation (the phenotype-fitness map) for exponential phage growth that allows an arbitrary distribution of lysis times and burst sizes. We also show that direct estimates of fitness are, in many cases, plausibly in error because the population has not attained stable age distribution and thus violates the model underlying the phenotype-fitness map. In conjunction with data provided here, the new understanding appears to resolve a discrepancy between the reported fitness of phage T7 and the substantially lower value calculated from its phenotype-fitness map