The effects of vegetation types and microhabitats on carabid beetle community composition in cool temperate Japan

The effects of vegetation types and environmental factors on carabid beetle (Coleoptera: Carabidae) communities were studied. Carabid beetles were collected using pitfall traps (total 2844 trapping days) and seven microenvironmental factors were measured in four vegetation types: grassland, natural evergreen coniferous forest (Pinus densiflora), deciduous broad-leaved natural forest (Quercus crispula, Betula platyphylla, Alnus japonica, or Fagus crenata), and deciduous coniferous plantation (Larix kaempferi) in cool temperate Japan. These four vegetation types provided a novel comparison between natural forests and plantations because the vast majority of related studies have investigated only deciduous broad-leaved natural forests and evergreen coniferous plantations. PERMANOVA indicated that vegetation types affected carabid community composition. Ordination plots showed that community composition differed greatly between grassland and forest vegetation types, but that community composition in the plantation forest overlapped with that of natural forest types. Characteristics differentiating the grassland included a high proportion of winged species and a low mean carabid body weight. Among the examined environmental factors, litter depth, soil water content, and depth of the soil A-horizon had large effects on carabid communities. These results suggest that the effect of afforestation on carabid communities in cool temperate Japan might be insignificant compared with the effects of cover types (deciduous vs. evergreen) and microenvironmental factors.     

Autophagy activation by novel inducers prevents BECN2-mediated drug tolerance to cannabinoids

Cannabinoids and related drugs generate profound behavioral effects (such as analgesic effects) through activating CNR1 (cannabinoid receptor 1 [brain]). However, repeated cannabinoid administration triggers lysosomal degradation of the receptor and rapid development of drug tolerance, limiting the medical use of marijuana in chronic diseases. The pathogenic mechanisms of cannabinoid tolerance are not fully understood, and little is known about its prevention. Here we show that a protein involved in macroautophagy/autophagy (a conserved lysosomal degradation pathway), BECN2 (beclin 2), mediates cannabinoid tolerance by preventing CNR1 recycling and resensitization after prolonged agonist exposure, and deletion of Becn2 rescues CNR1 activity in mouse brain and conveys resistance to analgesic tolerance to chronic cannabinoids. To target BECN2 therapeutically, we established a competitive recruitment model of BECN2 and identified novel synthetic, natural or physiological stimuli of autophagy that sequester BECN2 from its binding with GPRASP1, a receptor protein for CNR1 degradation. Co-administration of these autophagy inducers effectively restores the level and signaling of brain CNR1 and protects mice from developing tolerance to repeated cannabinoid usage. Overall, our findings demonstrate the functional link among autophagy, receptor signaling and animal behavior regulated by psychoactive drugs, and develop a new strategy to prevent tolerance and improve medical efficacy of cannabinoids by modulating the BECN2 interactome and autophagy activity.     

Global stability of obligate mutualism in community modules with facultative mutualists

Mutualism is a fundamental building block of ecological communities and an important driver of biotic evolution. Classic theory suggests that a pairwise two‐species obligate mutualism is fragile, with a large perturbation potentially driving both mutualist populations into extinction. In nature, however, there are many cases of pairwise obligate mutualism. Such pairwise obligate mutualisms are occasionally associated with additional interactions with facultative mutualists. Here, we use a mathematical model to show that when a two‐species obligate mutualism has a single additional link to a third facultative mutualist, the obligate mutualism can become permanently persistent. In the model, a facultative mutualist interacts with one of two inter‐dependent obligate mutualists, and the facultative mutualist enhances the persistence not only of its directly interacting obligate mutualist, but also that of the other obligate mutualist indirectly, enabling the permanent coexistence of the three mutualist species. The effect of the facultative mutualist is strong; it can allow a three‐species permanent coexistence even when two obligate mutualists by themselves are not sustainable (i.e. not locally stable). These results suggest that facultative mutualists can play a pivotal role for the persistence of obligate mutualisms, and contribute to a better understanding on the mechanisms maintaining more complex mutualistic networks of multiple species.     

Gene expression of Bacillus subtilis subtilisin E in Thermus thermophilus

The Bacillus subtilis subtilisin E gene was cloned into an expression vector of the extreme thermophile, Thermus thermophilus. Active subtilisin E was produced in E. coli, indicating that the Thermus promoter functions in E. coli. When the plasmid was further introduced into T. thermophilus, the subtilisin E gene was expressed and the gene product accumulated as an inactive pro-form, because the autoprocessing of the wild-type enzyme to the active-form did not occur at 50°C or above. Received 17 March 1999/ Accepted in revised form 28 June 1999     

The Nijmegen breakage syndrome gene and its role in genome stability

NBS1 is the key regulator of the RAD50/MRE11/NBS1 (R/M/N) protein complex, a sensor and mediator for cellular DNA damage response. NBS1 potentiates the enzymatic activity of MRE11 and directs the R/M/N complex to sites of DNA damage, where it forms nuclear foci by interacting with phosphorylated H2AX. The R/M/N complex also activates the ATM kinase, which is a major kinase involved in the activation of DNA damage signal pathways. The ATM requires the R/M/N complex for its own activation following DNA damage, and for conformational change to develop a high affinity for target proteins. In addition, association of NBS1 with PML, the promyelocytic leukemia protein, is required to form nuclear bodies, which have various functions depending on their location and composition. These nuclear bodies function not only in response to DNA damage, but are also involved in telomere maintenance when they are located on telomeres. In this review, we describe the role of NBS1 in the maintenance of genetic stability through the activation of cell-cycle checkpoints, DNA repair, and protein relocation.     

Comparison of Genomic and Epigenomic Expression in Monozygotic Twins Discordant for Rett Syndrome

Monozygotic (identical) twins have been widely used in genetic studies to determine the relative contributions of heredity and the environment in human diseases. Discordance in disease manifestation between affected monozygotic twins has been attributed to either environmental factors or different patterns of X chromosome inactivation (XCI). However, recent studies have identified genetic and epigenetic differences between monozygotic twins, thereby challenging the accepted experimental model for distinguishing the effects of nature and nurture. Here, we report the genomic and epigenomic sequences in skin fibroblasts of a discordant monozygotic twin pair with Rett syndrome, an X-linked neurodevelopmental disorder characterized by autistic features, epileptic seizures, gait ataxia and stereotypical hand movements. The twins shared the same de novo mutation in exon 4 of the MECP2 gene (G269AfsX288), which was paternal in origin and occurred during spermatogenesis. The XCI patterns in the twins did not differ in lymphocytes, skin fibroblasts, and hair cells (which originate from ectoderm as does neuronal tissue). No reproducible differences were detected between the twins in single nucleotide polymorphisms (SNPs), insertion-deletion polymorphisms (indels), or copy number variations. Differences in DNA methylation between the twins were detected in fibroblasts in the upstream regions of genes involved in brain function and skeletal tissues such as Mohawk Homeobox (MKX), Brain-type Creatine Kinase (CKB), and FYN Tyrosine Kinase Protooncogene (FYN). The level of methylation in these upstream regions was inversely correlated with the level of gene expression. Thus, differences in DNA methylation patterns likely underlie the discordance in Rett phenotypes between the twins.     

First observation of incomplete vertical circulation in Lake Biwa

Limnology - Vertical circulation reaches the bottom of the deepest (> 90 m) part of the northern basin of Lake Biwa, a warm monomictic lake, during winter (January to March)...     

Fast and Stable Proton Conduction in Heavily Scandium‐Doped Polycrystalline Barium Zirconate at Intermediate Temperatures

The environmental benefits of fuel cells and electrolyzers have become increasingly recognized in recent years. Fuel cells and electrolyzers that can operate at intermediate temperatures (300–450 °C) require, in principle, neither the precious metal catalysts that are typically used in polymer‐electrolyte‐membrane systems nor the costly heat‐resistant alloys used in balance‐of‐plant components of high‐temperature solid oxide electrochemical cells. These devices require an electrolyte with high ionic conductivity, typically more than 0.01 S cm^?1, and high chemical stability. To date, however, high ionic conductivities have been found in chemically unstable materials such as CsH₂PO₄, In‐doped SnP₂O₇, BaH₂, and LaH_3?2xO_x. Here, fast and stable proton conduction in 60‐at% Sc‐doped barium zirconate polycrystal, with a total conductivity of 0.01 S cm^?1 at 396 °C for 200 h is demonstrated. Heavy doping of Sc in barium zirconate simultaneously enhances the proton concentration, bulk proton diffusivity, specific grain boundary conductivity, and grain growth. An accelerated stability test under a highly concentrated and humidified CO₂ stream using in situ X‐ray diffraction shows that the perovskite phase is stable over 240 h at 400 °C under 0.98 atm of CO₂. These results show great promises as an electrolyte in solid‐state electrochemical devices operated at intermediate temperatures.     

Mutation design of a thermophilic Rubisco based on three‐dimensional structure enhances its activity at ambient temperature

Ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) plays a central role in carbon dioxide fixation on our planet. Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk‐Rubisco) shows approximately twenty times the activity of spinach Rubisco at high temperature, but only one‐eighth the activity at ambient temperature. We have tried to improve the activity of Tk‐Rubisco at ambient temperature, and have successfully constructed several mutants which showed higher activities than the wild‐type enzyme both in vitro and in vivo. Here, we designed new Tk‐Rubisco mutants based on its three‐dimensional structure and a sequence comparison of thermophilic and mesophilic plant Rubiscos. Four mutations were introduced to generate new mutants based on this strategy, and one of the four mutants, T289D, showed significantly improved activity compared to that of the wild‐type enzyme. The crystal structure of the Tk‐Rubisco T289D mutant suggested that the increase in activity was due to mechanisms distinct from those involved in the improvement in activity of Tk‐Rubisco SP8, a mutant protein previously reported to show the highest activity at ambient temperature. Combining the mutations of T289D and SP8 successfully generated a mutant protein (SP8‐T289D) with the highest activity to date both in vitro and in vivo. The improvement was particularly pronounced for the in vivo activity of SP8‐T289D when introduced into the mesophilic, photosynthetic bacterium Rhodopseudomonas palustris, which resulted in a strain with nearly two‐fold higher specific growth rates compared to that of a strain harboring the wild‐type enzyme at ambient temperature. Proteins 2016; 84:1339–1346. © 2016 Wiley Periodicals, Inc.     

Biological function of the pld gene product that degrades -poly-l-lysine in Streptomyces albulus

ε-Poly-l-lysine (ε-PL) is one of the few naturally occurring biopolymers and is characterized by a peptide bond between the α-carboxyl and ε-amino groups. Previously, we purified and characterized the ε-PL-degrading enzyme (Pld) from Streptomyces albulus, which is an ε-PL producer, and this enzyme was expected to confer self-resistance to the ε-PL produced by the organism itself. The gene encoding Pld was cloned based on the N-terminal amino acid sequence determined in this study, and a sequencing analysis revealed eight open reading frames (ORFs), i.e., ORF1 to ORF8 in the flanking region surrounding the pld gene (present in ORF5). To investigate the biological function of Pld, we constructed a knockout mutant in which the pld gene is inactivated. Studies on ε-PL susceptibility, ε-PL-degrading activity, and ε-PL productivity demonstrated that the pld gene does play a partial role in self-resistance and that S. albulus was found to produce other ε-PL-degrading enzyme(s) in addition to Pld. To the best of our knowledge, this is the first report on a self-resistance gene for a biopolymer possessing antibacterial activity.