Microevolution of the mitochondrial DNA control region in the Japanese brown bear (Ursus arctos) population.

We investigated nucleotide sequences of the mitochondrial DNA control region to describe natural genetic variations and to assess the relationships between subpopulations of the brown bear Ursus arctos on Hokkaido Island, Japan. Using the polymerase chain reaction product-direct sequencing technique, partial sequences (about 930 bases) of the control region were determined for 56 brown bears sampled throughout Hokkaido Island. A sequence alignment revealed that the brown bear control region included a variable sequence on the 5' side and a repetitive region on the 3' side. Phylogenetic trees reconstructed from the 5' variable region (696-702 bases) exhibited 17 haplotypes, which were clustered into three groups (Clusters A, B, and C). The distribution of each group did not overlap with those of the others, and the three different areas were located in separate mountainous forests of Hokkaido Island. Furthermore, most of the phylogenetically close haplotypes within each group were distributed geographically close to each other. In addition, the 3' repetitive region (arrays of 10 bases) exhibited a much faster mutation rate than the 5' variable region, resulting in heteroplasmy. Such mitochondrial DNA divergence in each group could have occurred after the brown bears migrated from the continent to Hokkaido and became fixed in the different areas.     

Finding the Factors of Reduced Genetic Diversity on X Chromosomes of Macaca fascicularis: Male-Driven Evolution,Demography, and Natural Selection

The ratio of genetic diversity on X chromosomes relative to autosomes in organisms with XX/XY sex chromosomes could provide fundamental insight into the process of genome evolution. Here we report this ratio for 24 cynomolgus monkeys (Macaca fascicularis) originating in Indonesia, Malaysia, and the Philippines. The average X/A diversity ratios in these samples was 0.34 and 0.20 in the Indonesian–Malaysian and Philippine populations, respectively, considerably lower than the null expectation of 0.75. A Philippine population supposed to derive from an ancestral population by founding events showed a significantly lower ratio than the parental population, suggesting a demographic effect for the reduction. Taking sex-specific mutation rate bias and demographic effect into account, expected X/A diversity ratios generated by computer simulations roughly agreed with the observed data in the intergenic regions. In contrast, silent sites in genic regions on X chromosomes showed strong reduction in genetic diversity and the observed X/A diversity ratio in the genic regions cannot be explained by mutation rate bias and demography, indicating that natural selection also reduces the level of polymorphism near genes. Whole-genome analysis of a female cynomolgus monkey also supported the notion of stronger reduction of genetic diversity near genes on the X chromosome.     

Caenorhabditis elegans glutamate transporter deletion induces AMPA-receptor/adenylyl cyclase 9-dependent excitotoxicity

In stroke and several neurodegenerative diseases, malfunction of glutamate (Glu) transporters causes Glu accumulation and triggers excitotoxicity. Many details on the cascade of events in the neurodegenerative process remain unclear. As molecular components of glutamatergic synapses are assembled in Caenorhabditis elegans and as many fundamental cellular processes are conserved from nematodes to humans, we studied Glu-induced necrosis in C. elegans and probed its genetic requirements. We combined Δglt-3 , a Glu transporter-null mutation, with expression of a constitutively active form of the alpha subunit of the G protein Gs. While neither Δglt-3 nor expression of the constitutively active form of the alpha subunit of the G protein Gs is severely toxic to C. elegans head interneurons, their combination induces extensive neurodegeneration. Δglt-3 -dependent neurodegeneration acts through Ca²⁺-permeable Glu receptors of the α-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid (AMPA) subtype, requires calreticulin function, and is modulated by calcineurin and type-9 adenylyl cyclase (AC9). We further show that mammalian AC9 hyperactivates mammalian AMPA-receptors (AMPA-Rs) in a Xenopus oocyte expression system, supporting that the relationship between AMPA-Rs hyperactivation and AC9 might be conserved between nematodes and mammals. AMPA-Rs–AC9 synergism is thus critical for nematode excitotoxicity and could potentially be involved in some forms of mammalian neurodegeneration.     

Sex-biased natal dispersal in Hokkaido brown bears revealed through mitochondrial DNA analysis

Understanding natal dispersal patterns is fundamental in the ecology and conservation biology of large wild carnivores. In this study, we used two approaches to determine genetic variation and dispersal patterns of brown bears in the Shiretoko Peninsula, eastern Hokkaido, Japan. The first approach was a large-scale genetic analysis. We analyzed haplotypes from the mitochondrial DNA (mtDNA) control region of 760 individual samples collected throughout the peninsula during 1998–2016. We detected seven haplotypes, including two that were confirmed for the first time. In females, the distribution of haplotypes was geographically structured, whereas haplotypes in males were distributed widely throughout the peninsula. Only some males in the lower peninsula had haplotypes that were not detected within the peninsula. The second approach was a local-scale genetic analysis, including intensive focal sampling in the Rusha area, a special wildlife protection area on the peninsula. Proportions of mtDNA haplotypes in adult bears were investigated and compared between the sexes. Although more than half of the females had the same haplotype, males had more diverse haplotypes, suggesting that they came to the Rusha area from other regions. Thus, our study revealed that mtDNA haplotype distribution has been maintained by female philopatry, and that bears exhibit male-biased dispersal. Furthermore, the lower peninsula appears to act as a contact zone between the peninsula and mainland Hokkaido, which is important for maintaining genetic diversity.     

High Free-Energy Barrier of 1D Diffusion Along DNA by Architectural DNA-Binding Proteins

Architectural DNA-binding proteins function to regulate diverse DNA reactions and have the defining property of significantly changing DNA conformation. Although the 1D movement along DNA by other types of DNA-binding proteins has been visualized, the mobility of architectural DNA-binding proteins on DNA remains unknown. Here, we applied single-molecule fluorescence imaging on arrays of extended DNA molecules to probe the binding dynamics of three structurally distinct architectural DNA-binding proteins: Nhp6A, HU, and Fis. Each of these proteins was observed to move along DNA, and the salt concentration independence of the 1D diffusion implies sliding with continuous contact to DNA. Nhp6A and HU exhibit a single sliding mode, whereas Fis exhibits two sliding modes. Based on comparison of the diffusion coefficients and sizes of many DNA binding proteins, the architectural proteins are categorized into a new group distinguished by an unusually high free-energy barrier for 1D diffusion. The higher free-energy barrier for 1D diffusion by architectural proteins can be attributed to the large DNA conformational changes that accompany binding and impede rotation-coupled movement along the DNA grooves.     

Cyanobacteria inhabiting biological soil crusts of a polar desert: Sør Rondane Mountains,Antarctica

Molecular and morphological methods were applied to study cyanobacterial community composition in biological soil crusts (BSCs) from four areas (two nunataks and two ridges) in the Sør Rondane Mountains, Antarctica. The sampling sites serve as control areas for open top chambers (OTCs) that were put in place in 2010 at the time of sample collection and will be compared with BSC samples taken from the OTCs in the future. Cyanobacterial cell biovolume was estimated using epifluorescence microscopy, which revealed the dominance of filamentous cyanobacteria in all studied sites except the Utsteinen ridge, where unicellular cyanobacteria were the most abundant. Cyanobacterial diversity was studied by a combination of molecular fingerprinting methods based on the 16S rRNA gene (denaturing gradient gel electrophoresis (DGGE) and 454 pyrosequencing) using cyanobacteria-specific primers. The number of DGGE sequences obtained per site was variable and, therefore, a high-throughput method was subsequently employed to improve the diversity coverage. Consistent with previous surveys in Antarctica, both methods showed that filamentous cyanobacteria, such as Leptolyngbya sp., Phormidium sp. and Microcoleus sp., were dominant in the studied sites.In addition, the studied localities differed in substrate type, climatic conditions and soil parameters, which probably resulted in differences in cyanobacterial community composition. Furthermore, the BSC growing on gneiss pebbles had lower cyanobacterial abundances than BSCs associated with granitic substrates.     

Growth-promoting effect of carbon material upon bacterial cells propagating through a distance

Carbon material such as graphite and activated charcoal, but not diamond, causes the promotion of growth of certain bacteria under ordinarily non-permissive stress conditions over a distance of several centimeters. Bacillus carboniphilus under the stress of a high KCl concentration and high temperature responded to this remote effect of carbon material with enhanced growth, and thermophile bacterium Bacillus stearothermophilus responded similarly yet moderately under the stress of low temperature. The remote effect of carbon was caused by its activation with external energy, probably of electromagnetic nature, as this effect was markedly decreased by sheltering the experimental system with an iron or aluminum barrier. Carbon material probably transforms the external oscillatory pulses or radiation into a signal exerting, far-reaching, growth-promoting effect upon cells. The most plausible candidate of signals emitted from carbon was considered to be (ultra)sonic.     

Intramolecular excitation energy transfer in diarylurea-linked zinc porphyrin-anthracene dyads.

Structurally controlled zinc porphyrin-anthracene dyads, syn-arranged 1 and anti-arranged 2, were newly synthesized employing a diarylurea linkage, and the excitation energy transfer (EET) from the anthracene to the zinc porphyrin chromophore was investigated by steady-state fluorescence emission spectroscopy as well as fluorescence lifetime measurement, especially focusing on the effect of the chromophoric orientation on the EET. In both of the dyads, intramolecular EET was facilitated upon excitation of the anthracene chromophore (lamda(ex)= 401 nm), and the zinc porphyrin S1-S0 emission (580-720 nm) was enhanced. The EET in the syn-arranged dyad 1 was more efficient than in the anti-arranged 2: the S1-S0 emission in 1 was 1.8 times larger than that in the zinc porphyrin reference compound 3, whereas that in 2 was enhanced by 1.6 times, compared to that in 3. In the fluorescence lifetime measurement, the quiet short-lived component assignable to the EET was observed for the dyads 1 and 2 beyond the analysis limit (<25 ps). The EET rate constants in the dyads 1 and 2 were estimated as not less than 4.0 x 10(10) s-1. However, in the case of 2, the residual long-lived component assigned to the anthracene emission was also observed at 425 nm. These results showed that the syn-arrangement of the zinc porphyrin and anthracene chromophores was more preferred for intramolecular EET to the anti-arrangement.