Transition from regular to chaos from the aspect of nodal domains associated with wave functions(2) Equilibrium and nonequilibrium statistical mechanics in systems showing chaos and quantum chaos, Chaos and Nonlinear Dynamics in Quantum-Mechanical and Macroscopic Systems)

この論文は国立情報学研究所の電子図書館事業により電子化されました。2次元4次振動子模型を用いて、系のダイナミクスが可積分からカオスまで変化するとき、波動関数の結節構造がどう変化するかを、結節領域の数、結節線と古典運動の境界との交点数、結節領域の面積分布の指標を用いて調べた

Plasmid Curing is a Promising Approach to Improve Thermophiles for Biotechnological Applications: Perspectives in Archaea

Thermophiles are attractive as host cells for microbial processes to produce or degrade various compounds. In these applications, it is often desirable to improve the properties of thermophiles, such as their growth rate, cell density, and protein productivity, although this is rarely achieved because of the lack of general approaches. In this chapter, we describe the elimination of the pHTA426 plasmid from a moderate thermophile, Geobacillus kaustophilus HTA426, and its effects on the microbial properties. This process, called plasmid curing, was simply achieved using a DNA intercalator and confirmed by phenotypic and genotypic analyses. Of note, pHTA426 curing had beneficial effects on diverse properties, probably because of the reduced energy burden in terms of plasmid replication at high temperatures. The result suggests that plasmid curing is a simple and versatile approach for improving thermophiles. In particular, this approach may be effective for archaeal thermophiles because they grow at much higher temperatures and could have the greater energy burden on plasmid replication. Data mining has also shown that plasmids are distributed in archaeal thermophiles. This chapter provides a new tip for improving archaeal thermophiles, thereby increasing the opportunities for their use in various biotechnological applications

Interaction network rewiring and species’ contributions to community-scale flexibility

「やわらかい」ネットワークを作るコア生物種 --生態系の柔軟性を支える種を探索する--. 京都大学プレスリリース. 2024-03-07.The architecture of species interaction networks is a key factor determining the stability of ecological communities. However, the fact that ecological network architecture can change through time is often overlooked in discussions on community-level processes, despite its theoretical importance. By compiling a time-series community dataset involving 50 spider species and 974 Hexapoda prey species/strains, we quantified the extent to which the architecture of predator–prey interaction networks could shift across time points. We then developed a framework for finding species that could increase the flexibility of the interaction network architecture. Those “network coordinator” species are expected to promote the persistence of species-rich ecological communities by buffering perturbations in communities. Although spiders are often considered as generalist predators, their contributions to network flexibility vary greatly among species. We also found that detritivorous prey species can be cores of interaction rewiring, dynamically interlinking below-ground and above-ground community dynamics. We further found that the predator–prey interactions between those network coordinators differed from those highlighted in the standard network-analytical framework assuming static topology. Analyses of network coordinators will add a new dimension to our understanding of species coexistence mechanisms and provide platforms for systematically prioritizing species in terms of their potential contributions in ecosystem conservation and restoration

Srs2 and RecQ homologs cooperate in mei-3-mediated homologous recombination repair of Neurospora crassa

Homologous recombination and post-replication repair facilitate restart of stalled or collapsed replication forks. The SRS2 gene of Saccharomyces cerevisiae encodes a 3′–5′ DNA helicase that functions both in homologous recombination repair and in post-replication repair. This study identifies and characterizes the SRS2 homolog in Neurospora crassa, which we call mus-50. A knockout mutant of N.crassa, mus-50, is sensitive to several DNA-damaging agents and genetic analyses indicate that it is epistatic with mei-3 (RAD51 homolog), mus-11 (RAD52 homolog), mus-48 (RAD55 homolog) and mus-49 (RAD57 homolog), suggesting a role for mus-50 in homologous recombination repair. However, epistasis evidence has presented that MUS50 does not participate in post-replication repair in N.crassa. Also, the N.crassa mus-25 (RAD54 homolog) mus-50 double mutant is viable, which is in contrast to the lethal phenotype of the equivalent rad54 srs2 mutant in S.cerevisiae. Tetrad analysis revealed that mus-50 in combination with mutations in two RecQ homologs, qde-3 and recQ2, is lethal, and this lethality is suppressed by mutation in mei-3, mus-11 or mus-25. Evidence is also presented for the two independent pathways for recovery from camptothecin-induced replication fork arrest: one pathway is dependent on QDE3 and MUS50 and the other pathway is dependent on MUS25 and RECQ2

Fluctuation properties of strength function associated with the giant quadrupole resonance in 208Pb

We performed fluctuation analysis by means of the local scaling dimension for the strength function of the isoscalar (IS) giant quadrupole resonance (GQR) in 208Pb where the strength function is obtained by the shell model calculation including 1p1h and 2p2h configurations. It is found that at almost all energy scales, fluctuation of the strength function obeys the Gaussian orthogonal ensemble (GOE) random matrix theory limit. This is contrasted with the results for the GQR in 40Ca, where at the intermediate energy scale about 1.7 MeV a deviation from the GOE limit was detected. It is found that the physical origin for this different behavior of the local scaling dimension is ascribed to the difference in the properties of the damping process.Comment: 10 pages, 14 figures, submitted to Physical Review

Latencies of Reflex Discharges in Some Oro-facial Reflexes of the Frog

Unitary reflex discharges were recorded from the branches of the trigeminal nerve innervating the submental and masseter muscles following electrical stimulation of the lingual branch of the glossopharyngeal nerve, the maxillary branch of the trigeminal nerve and the mandibular branch of the facial nerve. Reflex discharges were effectively elicited by repetitive electrical stimulation of afferent nerves, but the number of reflex impulses as well as the latencies varied from discharge to discharge. This suggests that the pathway of these reflexes is polysynaptic

Frequent Transposition of Multiple Insertion Sequences in Geobacillus kaustophilus HTA426

Geobacillus kaustophilus HTA426 is a thermophilic bacterium whose genome harbors numerous insertion sequences (IS). This study was initially conducted to generate mutant genes for thermostable T7 RNA polymerase in G. kaustophilus; however, relevant experiments unexpectedly identified that the organism transposed multiple IS elements and produced derivative cells that expressed a silent gene via transposition. The transposed elements were diverse and included members of the IS4, IS701, IS1634, and ISLre2 families. The transposition was relatively active at elevated temperatures and generated 4–9 bp of direct repeats at insertion sites. Transposition was more frequent in proliferative cells than in stationary cells but was comparable between both cells when sigX, which encodes an extra-cytoplasmic function sigma factor, was forcibly expressed. Southern blot analysis indicated that IS transposition occurred under growth inhibitory conditions by diverse stressors; however, IS transposition was not detected in cells that were cultured under growth non-inhibitory conditions. These observations suggest that G. kaustophilus enhances IS transposition via sigX-dependent stress responses when proliferative cells were prevented from active propagation. Considering Geobacillus spp. are highly adaptive bacteria that are remarkably distributed in diverse niches, it is possible that these organisms employ IS transposition for environmental adaptation via genetic diversification. Thus, this study provides new insights into adaptation strategies of Geobacillus spp. along with implications for strong codependence between mobile genetic elements and highly adaptive bacteria for stable persistence and evolutionary diversification, respectively. This is also the first report to reveal active IS elements at elevated temperatures in thermophiles and to suggest a sigma factor that governs IS transposition