The muscular dystrophic chicken is hypernatremic

1. The E3 ubiquitin protein ligase 1 (WWP1) gene, the mutation of which causes muscular dystrophy in chickens, is expressed not only in the pectoral muscle, but also in a number of tissues such as the kidney. Therefore, this study examined some parameters related to kidney function in muscular dystrophic (MD) chickens. 2. Plasma osmolality, Na⁺ and K⁺ concentrations, aldosterone levels, and the expression of aquaporin (AQP) 2, AQP3, and α subunits of the amiloride-sensitive epithelial sodium channel (αENaC) were analysed in the kidneys of 5-week-old MD chickens and White Leghorn (WL) chickens under physiological conditions or after one day of water deprivation. 3. Plasma osmolality, Na⁺ concentrations, and plasma aldosterone levels were significantly higher in MD chickens than in WL chickens. αENaC mRNA expression levels were lower in MD chickens than in WL chickens. AQP2 and AQP3 mRNA expression levels were similar in the two strains of chickens. 4. Plasma osmolality correlated with aldosterone levels and AQP2 and αENaC mRNA levels in WL chickens. In MD chickens, plasma osmolality correlated with AQP2 mRNA levels, but not with plasma aldosterone or αENaC mRNA levels. 5. These results suggest that neither water reabsorption nor the expression of AQP2 and AQP3 is impaired in MD chickens and that a WWP1 gene mutation may or may not directly induce an abnormality in Na⁺-reabsorption in the kidneys of MD chickens, potentially through αENaC.

Estimation of π-π Electronic Couplings from Current Measurements

The π-π interactions between organic molecules are among the most important parameters for optimizing the transport and optical properties of organic transistors, light-emitting diodes, and (bio-) molecular devices. Despite substantial theoretical progress, direct experimental measurement of the π-π electronic coupling energy parameter t has remained an old challenge due to molecular structural variability and the large number of parameters that affect the charge transport. Here, we propose a study of π-π interactions from electrochemical and current measurements on a large array of ferrocene-thiolated gold nanocrystals. We confirm the theoretical prediction that t can be assessed from a statistical analysis of current histograms. The extracted value of t ≈35 meV is in the expected range based on our density functional theory analysis. Furthermore, the t distribution is not necessarily Gaussian and could be used as an ultrasensitive technique to assess intermolecular distance fluctuation at the subangström level. The present work establishes a direct bridge between quantum chemistry, electrochemistry, organic electronics, and mesoscopic physics, all of which were used to discuss results and perspectives in a quantitative manner.

Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species

Nocardiosis caused by Nocardia seriolae is one of the major threats in the aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S. dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1 predicted genes, we found orthologs of virulence factors of pathogenic mycobacteria and human clinical Nocardia isolates involved in host cell invasion, modulation of phagocyte function and survival inside the macrophages. The virulence factor candidates provide an essential basis for understanding their pathogenic mechanisms at the molecular level by the fish nocardiosis research community in future studies. We also found many potential antibiotic resistance genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N. cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes were present in all five Nocardia genomes (core genes) and 1,982 genes were unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a greater number of mobile elements and genes of unknown function that comprise the differences in structure and gene content from the other Nocardia genomes. In addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC transport system. Because of limited resources in ocean environments, these N. seriolae UTF1 specific ABC transporters might facilitate adaptation strategies essential for marine environment survival. Thus, the availability of the complete N. seriolae UTF1 genome sequence will provide a valuable resource for comparative genomic studies of N. seriolae isolates, as well as provide new insights into the ecological and functional diversity of the genus Nocardia.

A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis

Bluefin tunas are one of the most important fishery resources worldwide. Because of high market values, bluefin tuna farming has been rapidly growing during recent years. At present, the most common form of the tuna farming is based on the stocking of wild-caught fish. Therefore, concerns have been raised about the negative impact of the tuna farming on wild stocks. Recently, the Pacific bluefin tuna (PBT), Thunnus orientalis, has succeeded in completing the reproduction cycle under aquaculture conditions, but production bottlenecks remain to be solved because of very little biological information on bluefin tunas. Functional genomics approaches promise to rapidly increase our knowledge on biological processes in the bluefin tuna. Here, we describe the development of the first 44K PBT oligonucleotide microarray (oligo-array), based on whole-genome shotgun (WGS) sequencing and large-scale expressed sequence tags (ESTs) data. In addition, we also introduce an initial 44K PBT oligo-array experiment using in vitro grown peripheral blood leukocytes (PBLs) stimulated with immunostimulants such as lipopolysaccharide (LPS: a cell wall component of Gram-negative bacteria) or polyinosinic:polycytidylic acid (poly I:C: a synthetic mimic of viral infection). This pilot 44K PBT oligo-array analysis successfully addressed distinct immune processes between LPS- and poly I:C- stimulated PBLs. Thus, we expect that this oligo-array will provide an excellent opportunity to analyze global gene expression profiles for a better understanding of diseases and stress, as well as for reproduction, development and influence of nutrition on tuna aquaculture production.

Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community

The nuclear 18S-rRNA gene has been used as a metabarcoding marker in massively parallel sequencing (MPS)-based environmental surveys for plankton biodiversity research. However, different hypervariable regions have been used in different studies, and their utility has been debated among researchers. In this study, detailed investigations into 18S-rRNA were carried out; we investigated the effective number of sequences deposited in international nucleotide sequence databases (INSDs), the amplification bias, and the amplicon sequence variability among the three variable regions, V1-3, V4-5 and V7-9, using in silico polymerase chain reaction (PCR) amplification based on INSDs. We also examined the primer universality and the taxonomic identification power, using MPS-based environmental surveys in the Sea of Okhotsk, to determine which region is more useful for MPS-based monitoring. The primer universality was not significantly different among the three regions, but the number of sequences deposited in INSDs was markedly larger for the V4-5 region than for the other two regions. The sequence variability was significantly different, with the highest variability in the V1-3 region, followed by the V7-9 region, and the lowest variability in the V4-5 region. The results of the MPS-based environmental surveys showed significantly higher identification power in the V1-3 and V7-9 regions than in the V4-5 region, but no significant difference was detected between the V1-3 and V7-9 regions. We therefore conclude that the V1-3 region will be the most suitable for future MPS-based monitoring of natural eukaryote communities, as the number of sequences deposited in INSDs increases.

Expressed sequence tag analyses of three leukocyte subpopulations in ayu Plecoglossus altivelis altivelis, separated by monoclonal antibodies

Ayu Plecoglossus altivelis altivelis are one of the most economically important fish for freshwater aquaculture in Japan. We conducted expressed sequence tag analyses of three leukocyte subpopulations, thrombocytes, neutrophils, and B lymphocytes in ayu using a next generation sequencer. The sequencing and de novo assembly yielded 22,494, 22,733, and 16,505 contigs from the thrombocyte, neutrophil, and B lymphocyte cDNA libraries, respectively. Pathways involving endocytosis, phagosomes, and lysosomes, were found in all three cDNA libraries using pathway analysis. The thrombocyte cDNA library contained 2894 unique sequences, including CXC chemokine receptor 4 and MHC class II. Cytokine and cytokine receptor genes such as interleukin (IL)-1β, IL-8, IL-1 receptor (IL-1R), IL-8RA, and IL-8RB were found among the 3056 unique sequences of the neutrophil cDNA library. Typical B lymphocyte related genes such as B cell linker protein, immunoglobulin (Ig) M, IgD and transforming growth factor β were found in the 1590 unique sequences of the B lymphocyte cDNA library. In summary, a large number of immune-related genes were identified from the three leukocyte cDNA libraries. Our results represent a valuable sequence resource for understanding the immune system function in ayu.

Valley polarization assisted spin polarization in two dimensions

Valleytronics is rapidly emerging as an exciting area of basic and applied research. In two-dimensional systems, valley polarization can dramatically modify physical properties through electron-electron interactions as demonstrated by such phenomena as the fractional quantum Hall effect and the metal-insulator transition. Here, we address the electrons' spin alignment in a magnetic field in silicon-on-insulator quantum wells under valley polarization. In stark contrast to expectations from a non-interacting model, we show experimentally that less magnetic field can be required to fully spin polarize a valley-polarized system than a valley-degenerate one. Furthermore, we show that these observations are quantitatively described by parameter-free ab initio quantum Monte Carlo simulations. We interpret the results as a manifestation of the greater stability of the spin- and valley-degenerate system against ferromagnetic instability and Wigner crystalization, which in turn suggests the existence of a new strongly correlated electron liquid at low electron densities.

Dispersive and dissipative coupling in a micromechanical resonator embedded with a nanomechanical resonator

A micromechanical resonator embedded with a nanomechanical resonator is developed whose dynamics can be captured by the coupled-Van der Pol-Duffing equations. Activating the nanomechanical resonator can dispersively shift the micromechanical resonance by more than 100 times its bandwidth and concurrently increase its energy dissipation rate to the point where it can even be deactivated. The coupled-Van der Pol-Duffing equations also suggest the possibility of self-oscillations. In the limit of strong excitation for the nanomechanical resonator, the dissipation in the micromechanical resonator can not only be reduced, resulting in a quality factor of >3× 10(6), it can even be eliminated entirely resulting in the micromechanical resonator spontaneously vibrating.

Cost-effective development of highly polymorphic microsatellite in Japanese quail facilitated by next-generation sequencing

Next-generation sequencing technologies permit rapid and cost-effective identification of numerous putative microsatellite loci. Here, from the genome sequences of Japanese quail, we developed microsatellite markers containing dinucleotide repeats and employed these for characterisation of genetic diversity and population structure. A total of 385 individuals from 12 experimental and one wild-derived Japanese quail lines were genotyped with newly developed autosomal markers. The maximum number of alleles, expected heterozygosity and polymorphic information content (PIC) per locus were 10, 0.80 and 0.77 respectively. Approximately half of the markers were highly informative (PIC ≥ 0.50). The mean number of alleles per locus and observed heterozygosity within a line were in the range of 1.3-4.1 and 0.11-0.53 respectively. Compared with the wild-derived line, genetic diversity levels were low in the experimental lines. Genetic differentiation (FST ) between all pairs of the lines ranged from 0.13 to 0.83. Genetic clustering analyses based on multilocus genotypes of individuals showed that most individuals formed clearly defined clusters corresponding to the origins of the lines. These results suggest that Japanese quail experimental lines are highly structured. Microsatellite markers developed in this study may be effective for future genetic studies of Japanese quail.

A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication

Background

Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication.

Results

We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication.

Conclusions

The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel.

A multimode electromechanical parametric resonator array

Electromechanical resonators have emerged as a versatile platform in which detectors with unprecedented sensitivities and quantum mechanics in a macroscopic context can be developed. These schemes invariably utilise a single resonator but increasingly the concept of an array of electromechanical resonators is promising a wealth of new possibilities. In spite of this, experimental realisations of such arrays have remained scarce due to the formidable challenges involved in their fabrication. In a variation to this approach, we identify 75 harmonic vibration modes in a single electromechanical resonator of which 7 can also be parametrically excited. The parametrically resonating modes exhibit vibrations with only 2 oscillation phases which are used to build a binary information array. We exploit this array to execute a mechanical byte memory, a shift-register and a controlled-NOT gate thus vividly illustrating the availability and functionality of an electromechanical resonator array by simply utilising higher order vibration modes.

Water electrolysis and energy harvesting with zero-dimensional ion-sensitive field-effect transistors

The relationship of the gas bubble size to the size distribution critically influences the effectiveness of electrochemical processes. Several optical and acoustical techniques have been used to characterize the size and emission frequency of bubbles. Here, we used zero-dimensional (0D) ion-sensitive field-effect transistors (ISFETs) buried under a microbath to detect the emission of individual bubbles electrically and to generate statistics on the bubble emission time. The bubble size was evaluated via a simple model of the electrolytic current. We suggest that energy lost during water electrolysis could be used to generate electric pulses at an optimal efficiency with an array of 0D ISFETs.

Efficacy of hypofractionated radiotherapy for nasal tumours in 38 dogs (2005-2008)

OBJECTIVES

To evaluate the efficacy of hypofractionated radiotherapy for canine nasal tumours, including the improvement in clinical signs, rate of complications and assessment of prognostic factors.

METHODS

Medical records of 38 dogs with malignant nasal tumours were reviewed, and those treated with a weekly schedule of hypofractionated radiotherapy were included in the study. Acute and late side effects were defined as complications noted either within 1 month or after 6 months of irradiation, respectively. Progression-free interval and overall survival were calculated using the Kaplan-Meier method. Log-rank test and Cox proportional hazard model were also performed.

RESULTS

Clinical signs improved in 30 of 36 dogs. Acute complications were seen in 28 of 36 dogs and were considered manageable. Late complications were observed in 17 of 30 dogs that survived 6 months or longer, but severe side effects were not observed. The median progression-free interval and overall survival was 245 days (95% CI: 127-512 days) and 512 days (95% CI: 203-820 days), respectively. Age, breed and presence of dyspnoea were negatively correlated with overall survival.

CLINICAL SIGNIFICANCE

These results suggest that hypofractionated radiotherapy could be a viable option for the treatment of nasal tumours in dogs that are not candidates for conventional multi-fractionated radiotherapy.

Phonon lasing in an electromechanical resonator

An electromechanical resonator harboring an atomlike spectrum of discrete mechanical vibrations, namely, phonon modes, has been developed. A purely mechanical three-mode system becomes available in the electromechanical atom in which the energy difference of the two higher modes is resonant with a long-lived lower mode. Our measurements reveal that even an incoherent input into the higher mode results in coherent emission in the lower mode that exhibits all the hallmarks of phonon lasing in a process that is reminiscent of Brillouin lasing.

Anomalous pressure effect in heteroacene organic field-effect transistors

Anomalous pressure dependent conductivity is revealed for heteroacene organic field-effect transistors of dinaphtho[2, 3-b:2', 3'-f]thieno[3, 2-b]thiophene single crystals in the direction of a and b crystallographic axes. In contrast to the normal characteristics of a monotonic increase in mobility μ with the application of external hydrostatic pressure P in conductors, we found that the present organic semiconductor devices exhibit nonmonotonic and gigantic pressure dependence including an even negative pressure coefficient dμ/dP. In combination with a structural analysis based on x-ray diffraction experiments under pressure, it is suggested that on-site molecular orientation and displacement peculiar in heteroacene molecules are responsible for the anomalous pressure effect.