Spatiotemporal patterns provoked by environmental variability in a predator–prey model

The emergence of spatiotemporal patterns in the distribution of species is one of the most striking phenomena in ecology and nonlinear science. Since it is known that spatial inhomogeneities can significantly affect the dynamics of ecological populations, in the present paper we investigate the impact of environmental variability on the formation of patterns in a spatially extended predator–prey model. In particular, we utilize a predator–prey system with a Holling III functional response and introduce random spatial variations of the kinetic parameter signifying the intrinsic growth rate of the prey, reflecting the impact of a heterogeneous environment. Our results reveal that in the proximity of the Hopf bifurcation environmental variability is able to provoke pattern formation, whereby the coherence of the patterns exhibits a resonance-like dependence on the variability strength. Furthermore, we show that the phenomenon can only be observed if the spatial heterogeneities exhibit large enough regions with high growth rates of the prey. Our findings thus indicate that variability could be an essential pattern formation mechanism of the populations.     

Wearing the veil: hijab,Islam and job qualifications as determinants of social attitudes towards immigrant women in Norway

Immigrant women are a particularly vulnerable part of the immigrant population. In this paper we analyse negative attitudes towards immigrant women in Norway. We focus on immigrant women’s formal job qualifications, their religious background and wearing of hijab – the headscarf sometimes used by Muslim women. Using survey-embedded experiments we are able to analyse the net effects on attitudes of job qualifications, Islamic religious background and the hijab. The results show that native population frequently has more negative views of Muslim women who wear a hijab. The negative effects of a hijab do not seem to be strongly reduced if a woman wearing it has higher education. With a single exception, the results also show that Muslim background in itself (i.e. without the hijab) does not have any strong effect on attitudes of the native population towards immigrant women.     

Peroxin Pex21p interacts with the C-terminal noncatalytic domain of yeast seryl-tRNA synthetase and forms a specific ternary complex with tRNA(Ser)

The seryl-tRNA synthetase from Saccharomyces cerevisiae interacts with the peroxisome biogenesis-related factor Pex21p. Several deletion mutants of seryl-tRNA synthetase were constructed and inspected for their ability to interact with Pex21p in a yeast two-hybrid assay, allowing mapping of the synthetase domain required for complex assembly. Deletion of the 13 C-terminal amino acids abolished Pex21p binding to seryl-tRNA synthetase. The catalytic parameters of purified truncated seryl-tRNA synthetase, determined in the serylation reaction, were found to be almost identical to those of the native enzyme. In vivo loss of interaction with Pex21p was confirmed in vitro by coaffinity purification. These data indicate that the C-terminally appended domain of yeast seryl-tRNA synthetase does not participate in substrate binding, but instead is required for association with Pex21p. We further determined that Pex21p does not directly bind tRNA, and nor does it possess a tRNA-binding motif, but it instead participates in the formation of a specific ternary complex with seryl-tRNA synthetase and tRNA(Ser), strengthening the interaction of seryl-tRNA synthetase with its cognate tRNA(Ser).     

Bacterial topoisomerase I and topoisomerase III relax supercoiled DNA via distinct pathways

Escherichia coli topoisomerases I and III (Topo I and Topo III) relax negatively supercoiled DNA and also catenate/decatenate DNA molecules containing single-stranded DNA regions. Although these enzymes share the same mechanism of action and have similar structures, they participate in different cellular processes. In bulk experiments Topo I is more efficient at DNA relaxation, whereas Topo III is more efficient at catenation/decatenation, probably reflecting their differing cellular roles. To examine the differences in the mechanism of these two related type IA topoisomerases, single-molecule relaxation studies were conducted on several DNA substrates: negatively supercoiled DNA, positively supercoiled DNA with a mismatch and positively supercoiled DNA with a bulge. The experiments show differences in the way the two proteins work at the single-molecule level, while also recovering observations from the bulk experiments. Overall, Topo III relaxes DNA efficiently in fast processive runs, but with long pauses before relaxation runs, whereas Topo I relaxes DNA in slow processive runs but with short pauses before runs. The combination of these properties results in Topo I having an overall faster total relaxation rate, even though the relaxation rate during a run for Topo III is much faster.     

Baeyer-Villiger oxidations of representative heterocyclic ketones by whole cells of engineered Escherichia coli expressing cyclohexanone monooxygenase

Whole cells of an Escherichia coli strain overexpressing Acinetobacter sp. NCIB 9871 cyclohexanone monooxygenase (CHMO; E.C. 1.14.13.22) have been used for the Baeyer-Villiger oxidation of representative heterocyclic six-membered ketones to probe the potential impact of nitrogen, sulfur and oxygen on the chemoselectivity of these reactions. The fact that all of these heterocyclic systems were accepted as substrates by the enzyme and gave normal Baeyer-Villiger products broadens the synthetic utility of the engineered E. coli strain and emphasizes the chemoselectivity achievable with enzymatic oxidation catalysts.     

Living organisms from Prigogine’s perspective: an opportunity to introduce students to biological entropy balance

All living structures, from archaea to human, are open thermodynamic systems analysed through nonequilibrium thermodynamics. Nonequilibrium thermodynamics is a field with important applications to life sciences, which is very often left out of life science courses. A three-step method is suggested to make an easy introduction of nonequilibrium thermodynamics to life science students. The first step is to introduce the Prigogine equation dS = d_eS + d_iS, and explain the meaning of the entropy exchange with the surroundings d_eS and internal entropy generation in the system d_iS. The second step is to show that the Prigogine equation is connected to the equilibrium thermodynamics already known to students. This can be done by deriving the Clausius inequality dS ≥ dq/T, from the Prigogine equation applied to reversible and irreversible processes in closed systems. Reversible and irreversible processes are discussed separately and the results are then combined into the Clausius inequality. The third step is to introduce the fact that the Prigogine equation has a variety of applications in life sciences. This would give the students an opportunity to understand the entropy balance of physiological processes in cells and organisms. The import and accumulation of entropy, entropy generation, and entropy export could be made easier for students to adopt.     

Age-associated decline in effective immune synapse formation of CD4(+) T cells is reversed by vitamin E supplementation

Aging is associated with reduced IL-2 production and T cell proliferation. Vitamin E supplementation, in aged animals and humans, increases cell division and IL-2 production by naive T cells. The immune synapse forms at the site of contact between a T cell and an APC and participates in T cell activation. We evaluated whether vitamin E affects the redistribution of signaling proteins to the immune synapse. Purified CD4(+) T cells, from the spleens of young and old mice, were treated with vitamin E before stimulation with a surrogate APC expressing anti-CD3. Using confocal fluorescent microscopy, we observed that CD4(+) T cells from old mice were significantly less likely to recruit signaling proteins to the immune synapse than cells from young mice. Vitamin E increased the percentage of old CD4(+) T cells capable of forming an effective immune synapse. Similar results were found following in vivo supplementation with vitamin E. When compared with memory cells, naive T cells from aged mice were more defective in immune synapse formation and were more responsive to vitamin E supplementation. These data show, for the first time, that vitamin E significantly improves age-related early T cell signaling events in naive CD4(+) T cells.     

Neural agrin controls maturation of the excitation-contraction coupling mechanism in human myotubes developing in vitro

The aim of this study was to elucidate the mechanisms responsible for the effects of innervation on the maturation of excitation-contraction coupling apparatus in human skeletal muscle. For this purpose, we compared the establishment of the excitation-contraction coupling mechanism in myotubes differentiated in four different experimental paradigms: 1) aneurally cultured, 2) cocultured with fetal rat spinal cord explants, 3) aneurally cultured in medium conditioned by cocultures, and 4) aneurally cultured in medium supplemented with purified recombinant chick neural agrin. Ca(2+) imaging indicated that coculturing human muscle cells with rat spinal cord explants increased the fraction of cells showing a functional excitation-contraction coupling mechanism. The effect of spinal cord explants was mimicked by treatment with medium conditioned by cocultures or by addition of 1 nM of recombinant neural agrin to the medium. The treatment with neural agrin increased the number of human muscle cells in which functional ryanodine receptors (RyRs) and dihydropyridine-sensitive L-type Ca(2+) channels were detectable. Our data are consistent with the hypothesis that agrin, released from neurons, controls the maturation of the excitation-contraction coupling mechanism and that this effect is due to modulation of both RyRs and L-type Ca(2+) channels. Thus, a novel role for neural agrin in skeletal muscle maturation is proposed.     

Thrombin inhibitors with novel P1 binding pocket functionality: free energy of binding analysis

The high incidence of thrombembolic diseases justifies the development of new antithrombotics. The search for a direct inhibitor has resulted in the synthesis of a considerable number of low molecular weight molecules that inhibit human α-thrombin potently. However, efforts to develop an orally active drug remain in progress as the most active inhibitors with a highly basic P1 moiety exhibit an unsatisfactory bioavailability profile. In our previous work we solved several X-ray structures of human α-thrombin in complexes with (1) novel bicyclic arginine mimetics attached to the glycylproline amide and pyridinone acetamide scaffold and (2) inhibitors with a novel aza scaffold and with charged or neutral P1 moieties. In the present contribution, we correlate the structures of the complex between these inhibitors and the protein with the calculated free energy of binding. The energy of solvation was calculated using the Poisson–Boltzmann approach. In particular, the requirements for successful recognition of an inhibitor at the protein’s active site pocket S1 are discussed. Figure We report here on free energy of binding analysis of thrombin inhibitors with novel aza scaffold and novel bicyclic arginine mimetics in S1 pocket of thrombin