Anna Wójcik

Selection in a cycling population : Differential response among skeletal traits

Abstract Population density cycles influence phenotypic evolution through both density‐dependent selection during periods of high density and through enhanced genetic drift during periods of low density. We investigated the response of different phenotypic traits to the same density cycles in a population of the yellow‐necked mouse, Apodemus flavicollis, from Białowieza National Park in Poland. We examined nonmetric skull traits, skull and mandible size, skull and mandible shape, and transferrin allele frequencies. We found that all of the traits changed significantly over the seven‐year study period. The greatest changes in nonmetric traits and mandible size occurred during periods of increasing density, and the magnitude of changes in skull and mandible shape was correlated with the magnitude of density changes. Frequencies of transferrin alleles changed the most when population density was in decline. Changes among the five phenotypic traits were generally uncorrelated with one another, except for skull and mandible shape. Nonmetric traits were selectively neutral when assessed with QST/FST analysis, whereas mandible size, mandible shape, and skull shape showed evidence of fairly strong selection. Selection on skull size was weak or nonexistent. We discuss how different assumptions about the genetic components of variance affect QST estimates when phenotypic variances are substituted for genetic ones. We also found that change in mandible size, mandible shape, skull size, and skull shape were greater than expected under a neutral model given reasonable assumptions about heritability and effective population size.

Role of Substrate Positioning in the Catalytic Reaction of 4-Hydroxyphenylpyruvate Dioxygenase-A QM/MM Study

Ring hydroxylation and coupled rearrangement reactions catalyzed by 4-hydroxyphenylpyruvate dioxygenase were studied with the QM/MM method ONIOM(B3LYP:AMBER). For electrophilic attack of the ferryl species on the aromatic ring, five channels were considered: attacks on the three ring atoms closest to the oxo ligand (C1, C2, C6) and insertion of oxygen across two bonds formed by them (C1-C2, C1-C6). For the subsequent migration of the carboxymethyl substituent, two possible directions were tested (C1→C2, C1→C6), and two different mechanisms were sought (stepwise radical, single-step heterolytic). In addition, formation of an epoxide (side)product and benzylic hydroxylation, as catalyzed by the closely related hydroxymandelate synthase, were investigated. From the computed reaction free energy profiles it follows that the most likely mechanism of 4-hydroxyphenylpyruvate dioxygenase involves electrophilic attack on the C1 carbon of the ring and subsequent single-step heterolytic migration of the substituent. Computed values of the kinetic isotope effect for this step are inverse, consistent with available experimental data. Electronic structure arguments for the preferred mechanism of attack on the ring are also presented.

Mechanism of O2 Activation by α-Ketoglutarate Dependent Oxygenases Revisited. A Quantum Chemical Study

Four mechanisms previously proposed for dioxygen activation catalyzed by α-keto acid dependent oxygenases (α-KAO) were studied with dispersion-corrected DFT methods employing B3LYP and TPSSh functionals in combination with triple-ζ basis set (cc-pVTZ). The aim of this study was to revisit mechanisms suggested in the past decade and resolve remaining issues related to dioxygen activation. Mechanism A, which runs on the quintet potential energy surface (PES) and includes formation of an Fe(III)-superoxide radical anion complex, subsequent oxidative decarboxylation, and O-O bond cleavage, was found to be most likely. However, mechanism B taking place on the septet PES involves a rate limiting barrier comparable to the one found for mechanism A, and thus it cannot be excluded, though two other mechanisms (C and D) were ruled out. Mechanism C is a minor variation of mechanism A, whereas mechanism D proceeds through formation of a triplet Fe(IV)-alkyl peroxo bridged intermediate. The study covered also full optimization of relevant minimum energy crossing points (MECPs). The relative energy of critical intermediates was also studied with the CCSD(T) method in order to benchmark TPSSh and B3LYP functionals with respect to their credibility in predicting relative energies of septet and triplet spin states of the ternary enzyme-Fe-α-keto glutarate (α-KG)-O2 complex.

Mating System and Reproductive Success in a Free-Living Population of the Bank Vole, Clethrionomys Glareolus

The mating system in a free-living population of the bank vole (Clethrionomys glareolus) was examined by mark-recapture and electrophoretic techniques. All overwintered animals from a spring population were sexually active. The home ranges of females were mutually exclusive; they adjoined or overlapped, on average, with 12.5 males. The home ranges of males were larger and overlapped extensively. Mean litter size was 5.8 pups. The mean interval between litters was 19.2 days with a high synchrony in parturition. On the basis of genotypic analysis the paternity of 13 litters was determined. Multiple paternity was not observed. Three males out of ten had offspring simultaneously with two females each. Reproductively successful males were not distinguishable from all available males by age, mass, or body size. However, in the groups of males competing for one female, the successful males were recognizable from competitors by being older and having smaller home ranges.

Mechanism of Benzylic Hydroxylation by 4-Hydroxymandelate Synthase. A Computational Study

Hydroxymandelate synthase (HMS) and 4-hydroxyphenylpyruvate dioxygenase (HPPD) are highly related enzymes using the same substrates but catalyzing hydroxylation reactions yielding different products. The first steps of the HMS and HPPD catalytic reactions are believed to proceed in the same way and lead to an Fe(IV)═O-hydroxyphenylacetate (HPA) intermediate. Further down the catalytic cycles, HMS uses Fe(IV)═O to perform hydroxylation of the benzylic carbon, whereas in HPPD, the reactive oxoferryl intermediate attacks the aromatic ring of HPA. This study focuses on this part of the HMS catalytic cycle that starts from the oxoferryl intermediate and aims to identify interactions within the active site that are responsible for enzyme specificity. To this end, a HMS-Fe(IV)═O-HPA complex was modeled with molecular dynamics simulations. On the basis of the molecular dynamics-equilibrated structure, an active site model suitable for quantum chemical investigations was constructed and used for density functional theory (B3LYP) calculations of the mechanism of the native reaction of HMS, i.e., benzylic hydroxylation, and the alternative electrophilic attack on the ring, which is a step of the HPPD catalytic cycle. The most important result of this study is the finding that the conformation of the Ser201 side chain in the second coordination shell has a key role in directing the reaction of Fe(IV)═O into either the HMS or the HPPD channel.

The alkenyl migration mechanism catalyzed by extradiol dioxygenases: a hybrid DFT study.

Abstract6-Hydroxymethyl-6-methylcyclohexa-2,4-dienone is a mechanistic probe which when incubated with an extradiol dioxygenase yields a 2-tropolone product. This observation was originally interpreted as evidence supporting a direct heterolytic 1,2-alkenyl migration mechanism for a ring expansion reaction catalyzed by this class of Fe(II)-dependent nonheme enzymes (Xin and Bugg in J Am Chem Soc 130:10422–10430, 2008). In the work reported in this contribution we used quantum chemical methods to test whether such a mechanism is energetically possible and we found that it is not, neither for the mechanistic probe nor for the native catalytic cycle intermediate. Models of increasing complexity were used to calculate energy barriers to the heterolytic 1,2-alkenyl migration and alternative radical mechanisms. It was found that the former involves substantially higher barriers than the latter. A tentative radical mechanism that accounts for the transformation of the probe substrate to 2-tropolone was also proposed, and it involves acceptable barriers.

Means to Facilitate the Overcoming of Gastric Juice Barrier by a Therapeutic Staphylococcal Bacteriophage A5/80

In this article we compare the efficacy of different pharmacological agents (ranitidine, and omeprazole) to support phage transit from stomach to distal portions of the gastrointestinal tract in rats. We show that a temporal modification of environment in the animal stomach may protect Twort-like therapeutic antistaphylococcal phage A5/80 (from bacteriophage collection of the Hirszfeld Institute of Immunology and Experimental Therapy PAS in Wroclaw, Poland) from the inactivation by gastric juice effectively enough to enable a significant fraction of orally administered A5/80 to pass to the intestine. Interestingly, we found that yogurt may be a relatively strong in enhancing phage transit. Given the immunomodulating activities of phages our data may suggest that phages and yogurt can act synergistically in mediating their probiotic activities and enhancing the effectiveness of oral phage therapy. We also demonstrate that orally applied phages of similar size, morphology, and sensitivity to acidic environment may differ in their translocation into the bloodstream. This was evident in mice in which a therapeutic staphylococcal phage A5/80 reached the blood upon oral administration combined with antacid agent whilst T4 phage was not detected even when applied in 103 times higher dose. Our findings also suggest that phage penetration from digestive tract to the blood may be species-specific.

Allozyme differentiation in four sympatric species of european shrews (Soricidae: Mammalia)

Abstract Four species of shrews from the Bialowieza Primeval Forest, eastern Poland, were analyzed electrophoretically: Sorex araneus Linnaeus, 1758, Sorex minutus Linnaeus, 1766, Neomys anomalus Cabrera, 1907, and Neomys fodiens (Pennant, 1771). Two of the 25 loci studied were monomorphic for the same allele in all species, nine loci were monomorphic for the same allele in both Sorex species and an alternate allele was fixed in the two species of Neomys . Only one locus ( Pgm-3 ) was diagnostic with a different allele in all species. The mean heterozygosity values in S. araneus and N. fodiens (0.069 and 0.061) were significantly higher than those in S. minutus and N. anomalus (0.021 and 0.029). The Neis genetic distances were small between the two Neomys species (0.123) and between the two Sorex species (0.330). The highest Neis distance was found between S. minutus and N. anomalus (2.487).

Microstructure and martensitic transformation in Ni48Mn39.5Sn12.5–xSix metamagnetic Heusler alloy ribbons

Abstract The paper describes the effect of Si for Sn substitution on microstructure and martensitic transformation in Ni48Mn39.5Sn12.5–xSix (x = 0, 1, 2) Heusler alloy ribbons. The evolution of phase transformation, structure and microstructural features were examined by means of differential scanning calorimetry, analytical transmission electron microscopy and high resolution electron microscopy. The alloys were induction melted, homogenized and subsequently rapidly solidified on a rotating copper wheel. The ribbons featured a two phase structure composed of the L21 parent phase and the martensite phase. Slight changes of the chemical composition in local areas of the studied samples were noticed. Such segregation was introduced by rapid quenching in response to different melting points of each element. This then had an effect on the local changes in the e/a ratio, effectively leading to nucleation of martensitic transformation in the affected areas.

Over-seasonal and sex-independent expression of kappa casein gene (CSN3) in mammalian blood lymphocytes.

After observing the nonspecific expression of the alpha S1 casein gene in peripheral blood mononuclear cells of goats, we continued to trace illegitimate gene-expression patterns in mammals. Six mammalian species (Bos taurus, Capra hircus, Ovis aries, Equus caballus, Sus scrofa, and Bison bonasus) were analyzed for the presence of kappa casein in peripheral blood mononuclear cells and Ficoll-isolated lymphocytes. To detect potential relationships between the expression pattern and reproductive status of the individual, the animals within species represented different sex, age, and physiological status (immature and reproducing males; immature, pregnant, lactating, and sterile females). Species-specific primers were designed for the two-step post reverse transcriptional-polymerase chain reaction. The products were sequenced and a Blast search performed. Transcripts of kappa casein were successfully detected in the peripheral blood mononuclear cells and lymphocytes of three of the species (goat, cow, and European bison). The presence of the transcripts was unrelated to sex, physiological status, or age of the animals.