Metallic State of a Mixed-Sequence Oligomer Salt That Models Doped PEDOT Family.

Modern organic conductors are typically low-molecular-weight or polymer-based materials. Low-molecular-weight materials can be characterized using crystallographic information, allowing structure-conductivity relationships to be established and conduction mechanisms to be understood. However, controlling their conductive properties through molecular structural modulation is often challenging because of their relatively narrow conjugate areas. In contrast, polymer-based materials have highly π-conjugated structures with wide molecular-weight distributions, and their structural inhomogeneity makes characterizing their structures difficult. Thus, we focused on the less-explored intermediate, i.e., single-molecular-weight oligomers that model doped poly(3,4-ethylenedioxythiophene) (PEDOT). The dimer and trimer models provided clear structures; however, the short oligomers led to much lower conductivities (<10-3 S cm-1) than that of doped PEDOT. Herein, we elongated the oligomer to a tetramer through geometrical tuning based on a mixed sequence. The "P-S-S-P" sequence (S: 3,4-ethylenedithiothiophene; P: 3,4-(2',2'-dimethypropylenedioxy)thiophene) with twisted S-S enhanced the solubility and chemical stability. The subsequent oxidation process planarized the oligomer and expanded the conjugate area. Interestingly, the sequence involving sterically bulky outer P units allowed the doped oligomer to form a pitched π-stack in the single-crystal form. This enabled the inclusion of excess counter anions, which modulated the band filling. The combined effects of conjugate area expansion and band-filling modulation significantly increased the room-temperature conductivity to 36 S cm-1. This is the highest value reported for a single-crystalline oligomer conductor. Furthermore, a metallic state was observed above room temperature in a single-crystalline oligoEDOT for the first time. This unique mixed-sequence strategy for oligomer-based conductors enabled the precise control of conductive properties.

Genes related to cell wall metabolisms are targeted by miRNAs in immature tomato fruits under drought stress.

The metabolism of tomato fruits changes when plants experience drought stress. In this study, we investigated changes in microRNA (miRNA) abundance and detected 32 miRNAs whose expression changes in fruit. The candidate target genes for each miRNA were predicted from the differentially expressed genes identified by transcriptome analysis at the same fruit maturation stage. The predicted targeted genes were related to cell wall metabolisms, response to pathogens, and plant hormones. Among these, we focused on cell wall metabolism-related genes and performed a dual luciferase assay to assess the targeting of their mRNAs by their predicted miRNA. As a result, sly-miR10532 and sly-miR7981e suppress the expression of mRNAs of galacturonosyltransferase-10 like encoding the main enzyme of pectin biosynthesis, while sly-miR171b-5p targets ß-1,3-glucosidase mRNAs involved in glucan degradation. These results will allow the systematic characterization of miRNA and their target genes in the tomato fruit under drought stress conditions.

A novel dimorphic microsporidian Ameson iseebi sp. nov. infecting muscle of the Japanese spiny lobster, Panulirus japonicus, in western Japan.

Japanese spiny lobsters (Panulirus japonicus) exhibiting white opaque abdominal muscle were found in Mie and Wakayama prefectures, in mid-Western Japan. Microscopically, two types of microsporidian spores, ovoid and rod-shaped, were observed infecting the muscle. Histologically, both types of spore were detected inside myofibers of the abdomen, appendages, and cardiac muscles and were often both observed in a single myofiber simultaneously. Transmission electron microscopy revealed that ovoid spores have villous projections on the surface, and that ovoid and rod-shaped spores have a polar filament with 12 coils and 6 to 8 coils respectively. Merogonic and sporogonic stages were observed around ovoid spores, but rarely around rod-shaped spores. The small subunit ribosomal DNA sequences obtained from both spore types were identical to each other, indicating that this microsporidian exhibits a clear spore dimorphism. Phylogenetic analysis based on the rDNA sequences indicates that this microsporidian is part of a clade consisting of the genera Ameson and Nadelspora, with the most closely related species being A. herrnkindi found in the Caribbean spiny lobster P. argus. Based on ultrastructural features, molecular phylogenetic data, host type and geographical differences among known species in these genera, the species found in whitened abdominal muscles of the Japanese spiny lobster is described as Ameson iseebi sp. nov.

High expression of GUS activities in sweet potato storage roots by sucrose-inducible minimal promoter.

KEY MESSAGE: We developed transgenic sweet potato with Spomin (sucrose-inducible minimal promoter)-GUS gene-fused constructs. Induced GUS activities by Spomin were higher than those by CaMV 35S promoter. We developed transgenic sweet potato (Ipomoea batatas L. Lam. cv. Kokei no. 14) plants with Spomin (sucrose-inducible minimal promoter)-GUS gene-fused constructs with signal peptides for sorting to cytosol, apoplast and ER, and we analyzed the GUS expression pattern of cut tissue after sucrose treatment. Induced GUS activities by Spomin were several hundred times higher than those by the CaMV 35S promoter. Also, GUS activities in storage roots induced with a Spomin-cytosol-GUS construct were higher than those with either Spomin-apoplast or -ER-GUS constructs. The induced GUS activities by Spomin were higher in storage roots without sucrose treatment than those with sucrose treatment. Chilling (4 °C) storage roots with Spomin constructs for 4 weeks produced higher GUS activities than in storage roots stored at 25 °C for 4 weeks. The calculated maximum GUS content in the storage roots was up to about 224.2 µg/g fresh weight. The chilling treatment increased the free sucrose content in the storage roots, and this increase in endogenous sugar levels induced increased GUS activities in the storage roots. Therefore, Spomin appears to be a useful promoter to develop protein production systems using sweet potato variety Kokei no. 14 storage roots by postharvest treatment.

Discovery of radioactive silver ((110m)Ag) in spiders and other fauna in the terrestrial environment after the meltdown of Fukushima Dai-ichi nuclear power plant.

Six months after the explosion of TEPCO's Fukushima Dai-ichi nuclear power plant, radioactive silver ((110m)Ag), was detected in concentrations of 3754 Bq/kg in Nephila clavata (the orb-web spider; Joro-gumo in Japanese) collected at Nimaibashi, Iitate village in Fukushima Prefecture, whereas (110m)Ag in the soil was 43.1 Bq/kg. A survey of 35 faunal species in the terrestrial environment during the 3.5 years after the accident showed that most of Anthropoda had two orders higher (110m)Ag in their tissues than soils, although silver is not an essential element for their life. However, tracing of the activity of (110m)Ag detected in spider Atypus karschi collected regularly at a fixed location showed that it declined much faster than the physical half-life. These results suggest that (110m)Ag was at once biologically concentrated by faunal species, especially Arthropoda, through food chain. The factors affecting the subsequent rapid decline of (110m)Ag concentration in faunal species are discussed.

A genome-wide association study identifies locus at 10q22 associated with clinical outcomes of adjuvant tamoxifen therapy for breast cancer patients in Japanese.

Although many association studies of polymorphisms in candidate genes with the clinical outcomes of breast cancer patients receiving adjuvant tamoxifen therapy have been reported, genetic factors determining individual response to tamoxifen are not fully understood. To identify genetic polymorphisms associated with clinical outcomes of patients with tamoxifen treatment, we conducted a genome-wide association study (GWAS). We studied 462 Japanese patients with hormone receptor-positive, invasive breast cancer receiving adjuvant tamoxifen therapy. Of them, 240 patients were analyzed by genome-wide genotyping using the Illumina Human610-Quad BeadChips, and two independent sets of 105 and 117 cases were used for replication studies. In the GWAS, we detected significant associations with recurrence-free survival at 15 single-nucleotide polymorphisms (SNPs) on nine chromosomal loci (1p31, 1q41, 5q33, 7p11, 10q22, 12q13, 13q22, 18q12 and 19p13) that satisfied a genome-wide significant threshold (log-rank P= 2.87 × 10(-9)-9.41 × 10(-8)). Among them, rs10509373 in C10orf11 gene on 10q22 was significantly associated with recurrence-free survival in the replication study (log-rank P= 2.02 × 10(-4)) and a combined analysis indicated a strong association of this SNP with recurrence-free survival in breast cancer patients treated with tamoxifen (log-rank P= 1.26 × 10(-10)). Hazard ratio per C allele of rs10509373 was 4.51 [95% confidence interval (CI), 2.72-7.51; P= 6.29 × 10(-9)]. In a combined analysis of rs10509373 genotype with previously identified genetic makers, CYP2D6 and ABCC2, the number of risk alleles of these three genes had cumulative effects on recurrence-free survival among 345 patients receiving tamoxifen monotherapy (log-rank P= 2.28 × 10(-12)). In conclusion, we identified a novel locus associated with recurrence-free survival in Japanese breast cancer patients receiving adjuvant tamoxifen therapy.

On the analytical solution for the Pütter-Bertalanffy growth equation.

This study develops the basic idea of Pütter and Bertalanffy addressing the allometric scaling of anabolism and catabolism on somatic growth dynamics. We proposed a standardized form of the Pütter-Bertalanffy equation (PBE), which is given as the extended model of Richards function, and subsequently solved it. The analytical solution of the PBE was defined by an incomplete beta function and can take a wide range of shapes in its growth curve. The mathematical behavior of PBE due to the change in parameter values was briefly discussed. Most forms of solution consistently hold the implicit functional type with respect to the variable of body size.

Remarkable shifts in the megabenthic community structure over four decades in Tokyo Bay, Japan, in relation to environmental variations.

We investigated long-term changes in the megabenthic community in Tokyo Bay, Japan, using data from fisheries-independent trawl surveys conducted from 1977 to 2023. In addition, we examined the potential relationship between changes in biotic communities and environmental conditions. The total abundance and biomass exhibited an increasing trend until 1987, followed by a substantial decline from the late 1980s to the 1990s due to a decrease in small to medium-sized fish and crustacean species. Meanwhile, a marked increase in the number of large fish (including elasmobranchs), mollusks, and echinoids, was observed in the 2000s. These shifts in the megabenthic community structure were correlated with an increase in water temperature and a decrease in nutrient concentrations and copepod densities. Cumulative evidence suggests that a remarkable shift in the megabenthic community structure occurred between the 1970s and the 2020s, which was possibly associated with variations in the environmental conditions in Tokyo Bay.

OsYSL16 plays a role in the allocation of iron.

Graminaceous plants acquire iron by secreting mugineic acid family phytosiderophores into the rhizosphere and taking up complexes of iron and phytosiderophores through YSL (yellow stripe 1-like) transporters. Rice OsYSL15 is a transporter of the iron(III)-2'-deoxymugineic acid complex. OsYSL16 has 85 % similarity to both OsYSL15 and the iron(II)-nicotianamine transporter OsYSL2. In the present study, we show that OsYSL16 functionally complemented a yeast mutant defective in iron uptake when grown on medium containing iron(III)-deoxymugineic acid, but not when grown on medium containing iron(II)-nicotianamine. OsYSL16-knockdown seedlings were smaller than wild-type seedlings when only iron(III)chloride was supplied as an iron source. The iron concentration in shoots of OsYSL16-knockdown plants was similar to that of the wild type; however, they showed more severe chlorosis than wild-type plants under iron-deficient conditions. Furthermore, OsYSL16-knockdown plants accumulated more iron in the vascular bundles of the leaves. Expression of the OsYSL16 promoter fused to the ß-glucuronidase gene showed that OsYSL16 is expressed in the root epidermis and vascular bundles of whole plants. The expression was typically observed around the xylem. In the vascular bundles of unelongated nodes, it was detected in the xylem of old leaves and the phloem of new leaves. Graminaceous plants translocate iron from the roots to old leaves mainly via the xylem and to new leaves mainly via the phloem. Our results suggest that OsYSL16 plays a role in the allocation of iron(III)-deoxymugineic acid via the vascular bundles.

A genome-wide association study identifies a genetic variant in the SIAH2 locus associated with hormonal receptor-positive breast cancer in Japanese.

In Japan, breast cancer is the most common cancer among women and the second leading cause of cancer death among women worldwide. To identify genetic variants associated with the disease susceptibility, we performed a genome-wide association study (GWAS) using a total of 1086 Japanese female patients with hormonal receptor-positive (HRP) breast cancer and 1816 female controls. We selected 33 single-nucleotide polymorphisms (SNPs) with suggestive associations in GWAS (P-value of <1 × 10(-4)) as well as 4 SNPs that were previously implicated their association with breast cancer for further replication by an independent set of 1653 cases and 2797 controls. We identified significant association of the disease with a SNP rs6788895 (P(combined) of 9.43 × 10(-8) with odds ratio (OR) of 1.22) in the SIAH2 (intron of seven in absentia homolog 2) gene on chromosome 3q25.1 where the involvement in estrogen-dependent diseases was suggested. In addition, rs3750817 in intron 2 of the fibroblast growth factor receptor 2 gene, which was reported to be associated with breast cancer susceptibility, was significantly replicated with P(combined) of 8.47 × 10(-8) with OR=1.22. Our results suggest a novel susceptibility locus on chromosome 3q25.1 for a HRP breast cancer.

Induction of systemic acquired resistance by heat shock treatment in Arabidopsis.

Systemic acquired resistance (SAR) is a potent innate immunity system in plants and has been used in rice fields. Development of SAR, involving priming, is achieved by activation of salicylic acid (SA)-mediated pathway. To determine whether heat shock (HS) treatment can induce SAR, we analyzed the effects of HS on Arabidopsis. HS treatment induced disease resistance, expression of SAR marker genes, and SA accumulation in wild-type but not in SA-deficient sid2 and NahG plants, indicating induction of SAR. Time course analysis of the effects of HS indicated that SAR was activated transiently, differently from biological induction, with a peak at 2-3 d after HS, and that it ceased in several days. Production of reactive oxygen species was observed before SA biosynthesis, which might be a trigger for SAR activation. The data presented here suggest that HS can induce SAR, but there exist unknown regulation mechanisms for the maintenance of SAR.

Low cadmium (LCD), a novel gene related to cadmium tolerance and accumulation in rice.

The contamination of food crops by cadmium (Cd) is a major concern in food production because it can reduce crop yields and threaten human health. In this study, knockout rice plants (Oryza sativa) tagged with the gene trap vector pGA2707 were screened for Cd tolerance, and the tolerant line lcd was obtained. The lcd mutant showed tolerance to Cd on agar plates and in hydroponic culture during early plant development. Metal concentration measurements in hydroponically grown plants revealed significantly less Cd in the shoots of lcd plants compared with wild-type (WT) shoots. When cultured in the field in soil artificially contaminated with low levels of Cd, lcd showed no significant difference in the Cd content of its leaf blades; however, the Cd concentration in the grains was 55% lower in 2009 and 43% lower in 2010. There were no significant differences in plant dry weight or seed yield between lcd and wild-type plants. LCD, a novel gene, is not homologous to any other known gene. LCD localized to the cytoplasm and nucleus, and was expressed mainly in the vascular tissues in the roots and phloem companion cells in the leaves. These data indicate that lcd may be useful for understanding Cd transport mechanisms and is a promising candidate rice line for use in combating the threat of Cd to human health.

Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus Chelarctus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.

Morphological descriptions of phyllosoma larvae are essential for correct species identification and investigating the spatiotemporal distribution and recruitment process of spiny and slipper lobsters. Species identification of the phyllosoma larvae in the Scyllarinae subfamily is particularly difficult because of the morphological similarities among species and the scarcity of morphological information describing correct species identity. We extracted mid-to final-stage (V to VIII) phyllosoma larvae (n = 12) belonging to the subfamily Scyllarinae from several plankton samples collected in the Pacific and then performed molecular species identification using mitochondrial DNA COI and 16S rDNA sequence analyses. Three larvae collected around the Ryukyu Archipelago were identified as Chelarctus aureus (stage VI to VIII), and four collected around the Ryukyu Archipelago and Ogasawara Islands were identified as C. virgosus (V to VIII). One larva (V) collected in the central South Pacific was determined to be a subspecies of C. crosnieri. DNA barcodes could not be made for the remaining four larvae (V to VIII) collected around the Ryukyu Archipelago (designated by ?Chelarctus sp-1). Based on the morphological characteristics of the C. virgosus phyllosoma described in this study and the adult distributions reported to date, C. cultrifer phyllosomas previously reported in Japanese and Taiwanese waters are likely to be C. virgosus. This paper also presents a set of diagnostic morphological characteristics that can be used to discriminate among these four species of Chelarctus and from other genera in the subfamily Scyllarinae.

Transcriptomic and Metabolomic Analyses Provide Insights into the Upregulation of Fatty Acid and Phospholipid Metabolism in Tomato Fruit under Drought Stress.

Transcriptome and metabolome analysis in tomato (Solanum lycopersicum) fruits cultivated under drought conditions showed that drought stress promoted fatty acid synthesis and increased the content of fatty acids in fruits. The accumulation of some phospholipids composed of palmitic acid and oleic acid also was significantly increased, especially in seeds. Moreover, inositol, which is a component of cell membranes and cell walls, was increased through the activity of the myoinositol monophosphatase 1-mediated pathway. In mature fruits, the levels of metabolic regulators such as ß-alanine and 4-aminobutyric acid were elevated. These results showed that these compounds are drought-responsive and enhance drought tolerance and subsequently they could enhance the nutritional value and health benefits of tomato fruit.

Lessons for pharmacogenomics studies: association study between CYP2D6 genotype and tamoxifen response.

We earlier reported a significant association between the cytochrome P450 2D6 (CYP2D6) genotype and the clinical outcome in 282 Japanese breast cancer patients receiving tamoxifen monotherapy. Although many research groups have provided evidence indicating the CYP2D6 genotype as one of the strongest predictors of tamoxifen response, the results still remain controversial. We hypothesized that concomitant treatment was one of the causes of these controversial results. We then studied 167 breast cancer patients who received tamoxifen-combined therapy to evaluate the effects of concomitant treatment on the association analysis and observed no significant association between CYP2D6 genotype and recurrence-free survival (P=0.44, hazard ratio: 0.64, 95% confidential interval: 0.20-1.99 in patients with two variant alleles vs. patients without a variant allele). When we carried out two subgroup analyses for nodal status and tumor size, we observed a positive association between the CYP2D6 genotype and the clinical outcome only in patients who received tamoxifen monotherapy. This study explained a part of the discrepancies among the reported results.

The spatial expression and regulation of transcription factors IDEF1 and IDEF2.

BACKGROUND AND AIMS: Under conditions of low iron availability, rice plants induce genes involved in iron uptake and utilization. The iron deficiency-responsive cis-acting element binding factors 1 and 2 (IDEF1 and IDEF2) regulate transcriptional response to iron deficiency in rice roots. Clarification of the functions of IDEF1 and IDEF2 could uncover the gene regulation mechanism. METHODS: Spatial patterns of IDEF1 and IDEF2 expression were analysed by histochemical staining of IDEF1 and IDEF2 promoter-GUS transgenic rice lines. Expression patterns of the target genes of IDEF1 and IDEF2 were analysed using transformants with induced or repressed expression of IDEF1 or IDEF2 grown in iron-rich or in iron-deficient solutions for 1 d. KEY RESULTS: IDEF1 and IDEF2 were highly expressed in the basal parts of the lateral roots and vascular bundles. IDEF1 and IDEF2 expression was dominant in leaf mesophyll and vascular cells, respectively. These expression patterns were similar under both iron-deficient and iron-sufficient conditions. IDEF1 was strongly expressed in pollen, ovaries, the aleurone layer and embryo. IDEF2 was expressed in pollen, ovaries and the dorsal vascular region of the endosperm. During seed germination, IDEF1 and IDEF2 were expressed in the endosperm and embryo. Expression of IDEF1 target genes was regulated in iron-rich roots similar to early iron-deficiency stages. In addition, the expression patterns of IDEF2 target genes were similar between iron-rich conditions and early or subsequent iron deficiency. CONCLUSIONS: IDEF1 and IDEF2 are constitutively expressed during both vegetative and reproductive stages. The spatial expression patterns of IDEF1 and IDEF2 overlap with their target genes in restricted cell types, but not in all cells. The spatial expression patterns and gene regulation of IDEF1 and IDEF2 in roots are generally conserved under conditions of iron sufficiency and deficiency, suggesting complicated interactions with unknown factors for sensing and transmitting iron-deficiency signals.

A highly sensitive, quick and simple quantification method for nicotianamine and 2'-deoxymugineic acid from minimum samples using LC/ESI-TOF-MS achieves functional analysis of these components in plants.

A highly sensitive quantitative method for assaying nicotianamine (NA) and 2'-deoxymugineic acid (DMA) using liquid chromatography/electrospray ionization time-of-flight mass spectrometry (LC/ESI-TOF-MS) was developed. The amino and hydroxyl groups of NA and DMA were derivatized using 9-fluorenylmethoxycarbonyl chloride. The amounts of NA and DMA in 10 mul of xylem sap from rice cultivated under iron (Fe)-sufficient and Fe-deficient conditions were quantified without concentration. In Fe-sufficient plants, the concentrations of NA and DMA were almost equal to that of Fe. In Fe-deficient plants, the concentration of NA did not change significantly, whereas that of DMA increased markedly.

Production of Ascaris suum As14 protein and its fusion protein with cholera toxin B subunit in rice seeds.

Plants are attractive vaccine production and oral delivery systems. Cereals are excellent candidate for edible vaccines, which can express and store high levels of proteins for extended periods of time without degradation. In this study, we produced a 14-kDa protective surface antigen of Ascaris suum L3 larvae and its fusion chimera with a mucosal carrier molecule cholera toxin B subunit (CTB) in rice (Oryza sativa L.) under the control of the endosperm-specific glutelin-B promoter. We found that the recombinant protein expression levels reached 1.5 microg per seed, a comparably high amount as compared to previously reported transgenic rice expression experiments. Potentials of transgenic rice plants as a source of oral vaccines against swine roundworm are discussed.

A size-structured matrix model to simulate dynamics of marine community size spectrum.

Several types of size-based models have been developed to model the size spectra of marine communities, in which abundance scales strongly with body size, using continuous differential equations. In this study, we develop a size-structured matrix model, which can be seen as a discretization of the Mckendrick-von Foerster equation, to simulate the dynamics of marine communities. The developed model uses a series of simple body size power functions to describe the basic processes of predator-prey interactions, reproduction, metabolism, and non-predation mortality based on the principle of mass balance. Linear size spectra with slopes of approximately -1 are successfully reproduced by this model. Several examples of numerical simulations are provided to demonstrate the model's behavior. Size spectra with cut-offs and/or waves are also found for certain parameter values. The matrix model is flexible and can be freely manipulated by users to answer different questions and is executed over a shorter numerical calculation running time than continuous models.

A novel growth function incorporating the effects of reproductive energy allocation.

Ontogenetic growth functions provide basic information in biological and ecological studies. Various growth functions classified into the Pütter model have been used historically, regardless of controversies over their appropriateness. Here, we present a novel growth function for fish and aquatic organisms (generalised q-VBGF) by considering an allocation schedule of allometrically produced surplus energy between somatic growth and reproduction. The generalised q-VBGF can track growth trajectories in different life history strategies from determinate to indeterminate growth by adjusting the value of the 'growth indeterminacy exponent' q. The timing of maturation and attainable body size can be adjusted by the 'maturation timing parameter' τ while maintaining a common growth trajectory before maturation. The generalised q-VBGF is a comprehensive growth function in which exponentials in the traditional monomolecular, von Bertalanffy, Gompertz, logistic, and Richards functions are replaced with q-exponentials defined in the non-extensive Tsallis statistics, and it fits to actual data more adequately than these conventional functions. The relationship between the estimated parameter values τ and rq forms a unique hyperbola, which provides a new insight into the continuum of life history strategies of organisms.