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SummaryGenetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of both positive and negative effects of mixed planting on plant resistance, called associational resistance and susceptibility. We used genome-wide polymorphisms of the plant speciesArabidopsis thalianato identify genotype pairs that enhance associational resistance to herbivory. By quantifying neighbor interactions among 199 genotypes grown in a randomized block design, we predicted that 823 of the 19,701 candidate pairs could reduce herbivory through associational resistance. We planted such pairs with predicted associational resistance in mixtures and monocultures and found a significant reduction in herbivore damage in the mixtures. Our study highlights the potential application to assemble genotype mixtures with positive biodiversity effects.

Purpose Although reports suggest that the pancreatic volume decreases after gastrectomy for gastric cancer, the relationship between the pancreatic volume and secretory function after gastrectomy remains unclear. In this study, we examined the relationship between the pancreatic volume and exocrine and endocrine functions after total gastrectomy. Methods The pancreatic volumes of 18 distal gastrectomy and 15 total gastrectomy patients were retrospectively measured using computed tomography volumetry up to 5 years postoperatively. Ten low anterior resection patients were selected as controls. In addition, the pancreatic volume and exocrine function evaluated by fecal elastase and the insulin secretory function evaluated by glucagon tolerance testing were prospectively examined before and one year after surgery in nine cases of total gastrectomy. Results After low anterior resection, the pancreatic volume did not change, but after distal and total gastrectomy, the pancreatic volume decreased continuously until the fifth year. After total gastrectomy, fecal elastase decreased significantly from 865.8 μg/g to 603.2 μg/g in the first year (p = 0.0316), and the insulin secretion capacity also decreased significantly from 3.83 ng/mL to 2.26 ng/mL (p = 0.0019). Conclusions The pancreatic volume decreases continuously after gastrectomy for gastric cancer, and the pancreatic exocrine and endocrine functions decrease along with pancreatic atrophy after total gastrectomy.

Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers, but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software to analyze field images, where the plant shape, color, and background vary over months. We estimated the anthocyanin contents of small individuals of fourArabidopsisspecies using color information and verified the results experimentally. We obtained >4 million plant images over three field seasons to study anthocyanin fluctuations. We found significant effects of past radiation, coldness, and precipitation on the anthocyanin content in the field. The synthetic allopolyploidA. kamchaticarecapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation pipeline facilitates the study of plant responses to complex environments termed “in natura.”

Excessive amounts of metal ions in soil are toxic for most plant species, yet metal can also facilitate plant survival by elemental defense against herbivores and pathogens. Zinc and cadmium hyperaccumulation in Arabidopsis halleri is known to be effective for the defense against natural enemies. The allotetraploid species A. kamchatica, derived from A. halleri and a non‐hyperaccumulator A. lyrata, has a lower hyperaccumulation level of zinc than A. halleri, but its significance for elemental defense remains unknown. In this study, we evaluated the accumulation levels of zinc and cadmium in the allotetraploid compared with its diploid progenitors, and evaluated the contribution of metal treatments to anti‐herbivore resistance under field conditions. The accumulation level of zinc in A. kamchatica was intermediate between the progenitors, but that of cadmium was lower than in both diploid progenitors. The elemental defense of A. kamchatica and A. halleri was supported by a field experiment comparing the herbivory level between a control group and metal‐supplemented plants. Moreover, the effect of elemental defense was lower in A. kamchatica than in the hyperaccumulator progenitor A. halleri, which is consistent with the metal accumulation level. This result reveals that the allotetraploid plant inherited its hyperaccumulating ability from one progenitor as an advantageous trait but at an intermediate level.

Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.

Wild Japanese macaques (Macaca fuscata Blyth) living in the highland and lowland areas of Yakushima are known to have different diets, with highland individuals consuming more leaves. We aim to clarify whether and how these differences in diet are also reflected by gut microbial composition and fermentation ability. Therefore, we conduct an in vitro fermentation assay using fresh feces from macaques as inoculum and dry leaf powder of Eurya japonica Thunb. as a substrate. Fermentation activity was higher for feces collected in the highland, as evidenced by higher gas and butyric acid production and lower pH. Genetic analysis indicated separation of highland and lowland in terms of both community structure and function of the gut microbiota. Comparison of feces and suspension after fermentation indicated that the community structure changed during fermentation, and the change was larger for lowland samples. Analysis of the 16S rRNA V3-V4 barcoding region of the gut microbiota showed that community structure was clearly clustered between the two areas. Furthermore, metagenomic analysis indicated separation by gene and pathway abundance patterns. Two pathways (glycogen biosynthesis I and D-galacturonate degradation I) were enriched in lowland samples, possibly related to the fruit-eating lifestyle in the lowland. Overall, we demonstrated that the more leaf-eating highland Japanese macaques harbor gut microbiota with higher leaf fermentation ability compared with the more fruit-eating lowland ones. Broad, non-specific taxonomic and functional gut microbiome differences suggest that this pattern may be driven by a complex interplay between many taxa and pathways rather than single functional traits.

A 75-year-old woman with a history of postoperative chemotherapy for lung adenocarcinoma and a history of Helicobacter pylori eradication for idiopathic thrombocytopenic purpura (ITP) was admitted to the department of hematology and oncology for the treatment of anemia 2 weeks after BNT162b2 mRNA COVID-19 vaccination. Her blood examination revealed direct and indirect Coombs test-positive hemolytic anemia and elevation of serum LDH and indirect bilirubin levels. No obvious trigger other than BNT162b2 mRNA COVID-19 vaccination was found. She was diagnosed with autoimmune hemolytic anemia (AIHA), and oral prednisolone therapy was administered. The anemia improved soon after the administration of prednisolone. Although vaccination is considered to be very important for suppressing the spread of COVID-19, there have been reports of increasing risk of ITP development and deterioration caused by BNT162b2 mRNA COVID-19 vaccination. Because the number of vaccinated people is increasing rapidly, hematologists must be vigilant to the development of AIHA after BNT162b2 mRNA COVID-19 vaccination although case reports of this phenomenon have been very rare thus far.

Interspecific gene flow by hybridization may weaken species barriers and adaptive divergence, but can also initiate reinforcement of reproductive isolation trough natural and sexual selection. The extent of interspecific gene flow and its consequences for the initiation and maintenance of species barriers in natural systems remain poorly understood, however. To assess genome-wide patterns of gene flow between the two closely related European dung fly species Sepsis cynipsea and Sepsis neocynipsea (Diptera: Sepsidae), we tested for historical gene flow with the aid of ABBA-BABA test using whole-genome resequencing data from pooled DNA of male specimens originating from natural and laboratory populations. We contrasted genome-wide variation in DNA sequence differences between samples from sympatric populations of the two species in France and Switzerland with that of interspecific differences between pairs of samples involving allopatric populations from Estonia and Italy. In the French Cevennes, we detected a relative excess of DNA sequence identity, suggesting interspecific gene flow in sympatry. In contrast, at two sites in Switzerland, we observed a relative depletion of DNA sequence identity compatible with reinforcement of species boundaries in sympatry. Our results suggest that the species boundaries between S. cynipsea and S. neocynipsea in Europe depend on the eco-geographic context.

Background: Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its underlying molecular mechanisms. Particular attention was given to allopolyploid study systems, species resulting from an hybridization event accompanied by WGD. Investigating the mechanisms behind the survival of a newly formed allopolyploid highlighted the key role of DNA methylation. With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution. However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process. To overcome these problems, we developed the Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (ARPEGGIO): the first workflow for the analysis of epigenetic data in polyploids. This workflow analyzes WGBS data from allopolyploid species via the genome assemblies of the allopolyploid’s parent species. ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes. ARPEGGIO offers automation, but more importantly, a complete set of analyses including spot checks starting from raw WGBS data: quality checks, trimming, alignment, methylation extraction, statistical analyses and downstream analyses. A full run of ARPEGGIO outputs a list of genes showing differential methylation. ARPEGGIO was made simple to set up, run and interpret, and its implementation ensures reproducibility by including both package management and containerization. Results: We evaluated ARPEGGIO in two ways. First, we tested EAGLE-RC’s performance with publicly available datasets given a ground truth, and we show that EAGLE-RC decreases the error rate by 3 to 4 times compared to standard approaches. Second, using the same initial dataset, we show agreement between ARPEGGIO’s output and published results. Compared to other similar workflows, ARPEGGIO is the only one supporting polyploid data. Conclusions: The goal of ARPEGGIO is to promote, support and improve polyploid research with a reproducible and automated set of analyses in a convenient implementation. ARPEGGIO is available at https://github.com/supermaxiste/ARPEGGIO., MC genomics, 22 (1), ISSN:1471-2164

Complex cell shapes are generated first by breaking symmetry, and subsequent polar growth. Localized bending of anticlinal walls initiates lobe formation in the epidermal pavement cells of cotyledons and leaves, but how the microtubule cytoskeleton mediates local cell growth, and how plant pavement cells benefit from adopting jigsaw puzzle-like shapes, are poorly understood. In Arabidopsis (Arabidopsis thaliana), the basic Pro-rich protein (BPP) microtubule-associated protein family comprises seven members. We analyzed lobe morphogenesis in cotyledon pavement cells of a BPP1;BPP2;BPP5 triple knockout mutant. New image analysis methods (MtCurv and BQuant) showed that anticlinal microtubule bundles were significantly reduced and cortical microtubules that fan out radially across the periclinal wall did not enrich at the convex side of developing lobes. Despite these microtubule defects, new lobes were initiated at the same frequency as in wild-type cells, but they did not expand into well-defined protrusions. Eventually, mutant cells formed nearly polygonal shapes and adopted concentric microtubule patterns. The mutant periclinal cell wall bulged outward. The radius of the calculated inscribed circle of the pavement cells, a proposed proxy for maximal stress in the cell wall, was consistently larger in the mutant cells during cotyledon development, and correlated with an increase in cell height. These bpp mutant phenotypes provide genetic and cell biological evidence that initiation and growth of lobes are distinct morphogenetic processes, and that interdigitated cell geometry effectively suppresses large outward bulging of pavement cells.

Chemolithoautotrophic bacterium Ralstonia eutropha is a versatile host for production of various useful compounds including polyhydroxyalkanoates (PHAs) under both heterotrophic and autotrophic conditions. In this bacterium, Calvin-Benson-Bassham (CBB) cycle is functional even under heterotrophic conditions on sugars and reutilizes CO

Contemporary speciation provides a unique opportunity to directly observe the traits and environmental responses of a new species. Cardamine insueta is an allotriploid species that appeared within the past 150 years in a Swiss village, Urnerboden. In contrast to its two progenitor species, Cardamine amara and Cardamine rivularis that live in wet and open habitats, respectively, C. insueta is found in-between their habitats with temporal water level fluctuation. This triploid species propagates clonally and serves as a triploid bridge to form higher ploidy species. Although niche separation is observed in field studies, the mechanisms underlying the environmental robustness of C. insueta are not clear. To characterize responses to a fluctuating environment, we performed a time-course analysis of homeolog gene expression in C. insueta in response to submergence treatment. For this purpose, the two parental (C. amara and C. rivularis) genome sequences were assembled with a reference-guided approach, and homeolog-specific gene expression was quantified using HomeoRoq software. We found that C. insueta and C. rivularis initiated vegetative propagation by forming ectopic meristems on leaves, while C. amara did not. We examined homeolog-specific gene expression of three species at nine time points during the treatment. The genome-wide expression ratio of homeolog pairs was 2:1 over the time-course, consistent with the ploidy number. By searching the genes with high coefficient of variation of expression over time-course transcriptome data, we found many known key transcriptional factors related to meristem development and formation upregulated in both C. rivularis and rivularis-homeolog of C. insueta, but not in C. amara. Moreover, some amara-homeologs of these genes were also upregulated in the triploid, suggesting trans-regulation. In turn, Gene Ontology analysis suggested that the expression pattern of submergence tolerant genes in the triploid was inherited from C. amara. These results suggest that the triploid C. insueta combined advantageous patterns of parental transcriptomes to contribute to its establishment in a new niche along a water-usage gradient.

Population genetics studies of allopolyploid species lag behind those of diploid species because of practical difficulties in analysis of homeologs-duplicated gene copies originating from hybridized parental species. Pool-Seq, i.e. massive parallel sequencing of pooled individuals, has high potential for detecting nucleotide polymorphisms within and among multiple populations; however, its use has been limited to diploid species. We applied Pool-Seq to an allopolyploid species by developing a bioinformatic pipeline that assigns reads to each homeolog as well as to each polymorphic allele within each homeolog. We simultaneously sequenced eight genes from twenty individuals from each of 24 populations, and found over 100 polymorphic sites in each homeolog. For two sites, we estimated allele frequencies using the number of reads and then validated these estimations by making individual-based estimations. Pool-Seq using our bioinformatic pipeline allows efficient evaluation of nucleotide polymorphisms in a large number of individuals, even in allopolyploid species.

Recently, increasing attempts have been made to understand how plant genes function in natura. In this context, transcriptional profiles represent plant physiological status in response to environmental stimuli. Herein, we combined high-throughput RNA-Seq with insect survey data on 19 accessions of Arabidopsis thaliana grown at a field site in Switzerland. We found that genes with the gene ontology (GO) annotations of “glucosinolate biosynthetic process” and “response to insects” were most significantly enriched, and the expression of these genes was highly variable among plant accessions. Nearly half of the total expression variation in the glucosinolate biosynthetic genes (AOPs, ESM1, ESP, and TGG1) was explained by among-accession variation. Of these genes, the expression level of AOP3 differed among Col-0 accession individuals depending on the abundance of the mustard aphid (Lipaphis erysimi). We also found that the expression of the major cis-jasmone activated gene CYP81D11 was positively correlated with the number of flea beetles (Phyllotreta striolata and Phyllotreta atra). Combined with the field RNA-Seq data, bioassays confirmed that AOP3 was up-regulated in response to attack by mustard aphids. The combined results from RNA-Seq and our ecological survey illustrate the feasibility of using field transcriptomics to detect an inducible defense, providing a first step towards an in natura understanding of biotic interactions involving phenotypic plasticity.

Although Pneumocystis pneumonia (PCP), a life-threatening infection, has been reported in patients with non-Hodgkin B-cell lymphoma (BNHL) who were treated with rituximab-containing chemotherapies (R-CTX), the PCP prophylaxis regimen awaits establishment to date. This study reports a retrospective analysis of the efficacy and safety of a low-dose trimethoprim/sulfamethoxazole (TMP/SMX) in patients with BNHL receiving R-CTX. We retrospectively analyzed 156 patients newly diagnosed with BNHL who received R-CTX at our institute from 2010 to 2015. We collected patients' clinical and laboratory data, including lymphocytes count, IgG level, PCP prophylaxis regimens, and adverse events (AEs). Patients were categorized into the following two groups based on the TMP/SMX regimen: group A (33 patients; 80 mg/400 mg×3/week) or group B (65 patients; 160 mg/800 mg×2/week). Both lymphocytes count and IgG level declined during R-CTX. No patient developed PCP. Patients in group B exhibited a significantly higher incidence of AEs (18.2% vs. 63.1%; p0.05) and increased AST (6.1% vs. 26.6%; p0.05), compared with those in group A. Thus, TMP/SMX (80 mg/400 mg×3/week) effectively prevents PCP and is preferable because of the lower rates of AEs.

Recently, increasing attempts have been made to understand how plant genes function in natura. In this context, transcriptional profiles represent plant physiological status in response to environmental stimuli. Herein, we combined high-throughput RNA-Seq with insect survey data on 19 accessions of Arabidopsis thaliana grown at a field site in Switzerland. We found that genes with the gene ontology (GO) annotations of “glucosinolate biosynthetic process” and “response to insects” were most significantly enriched, and the expression of these genes was highly variable among plant accessions. Nearly half of the total expression variation in the glucosinolate biosynthetic genes (AOPs, ESM1, ESP, and TGG1) was explained by among-accession variation. Of these genes, the expression level of AOP3 differed among Col-0 accession individuals depending on the abundance of the mustard aphid (Lipaphis erysimi). We also found that the expression of the major cis-jasmone activated gene CYP81D11 was positively correlated with the number of flea beetles (Phyllotreta striolata and Phyllotreta atra). Combined with the field RNA-Seq data, bioassays confirmed that AOP3 was up-regulated in response to attack by mustard aphids. The combined results from RNA-Seq and our ecological survey illustrate the feasibility of using field transcriptomics to detect an inducible defense, providing a first step towards an in natura understanding of biotic interactions involving phenotypic plasticity.

The self-incompatible species Arabidopsis halleri is a close relative of the self-compatible model plant Arabidopsis thaliana. The broad European and Asian distribution and heavy metal hyperaccumulation ability make A. halleri a useful model for ecological genomics studies. We used long-insert mate-pair libraries to improve the genome assembly of the A. halleri ssp. gemmifera Tada mine genotype (W302) collected from a site with high contamination by heavy metals in Japan. After five rounds of forced selfing, heterozygosity was reduced to 0.04%, which facilitated subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the estimated genome size and achieved scaffold N50 length of 712 kb. To validate assembly and annotation, we used synteny of A. halleri Tada mine with a previously published high-quality reference assembly of a closely related species, Arabidopsis lyrata. Further validation of the assembly quality comes from synteny and phylogenetic analysis of the HEAVY METAL ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published sequences from European A. halleri for comparison. Three tandemly duplicated copies of HMA4, key gene involved in cadmium and zinc hyperaccumulation, were assembled on a single scaffold. The assembly will enhance the genomewide studies of A. halleri as well as the allopolyploid Arabidopsis kamchatica derived from A. lyrata and A. halleri.

The habitats of polyploid species are generally distinct from their parental species. Stebbins described polyploids as 'general purpose genotypes', which can tolerate a wide range of environmental conditions. However, little is known about its molecular basis because of the complexity of polyploid genomes. We hypothesized that allopolyploid species might utilize the expression patterns of both parents depending on environments (polyploid plasticity hypothesis). We focused on hydrological niche segregation along fine-scale soil moisture and waterlogging gradients. Two diploid species, Cardamine amara and Cardamine hirsuta, grew best in submerged and unsubmerged conditions, respectively, consistent with their natural habitats. Interestingly, the allotetraploid Cardamine flexuosa derived from them grew similarly in fluctuating as well as submerged and unsubmerged conditions, consistent with its wide environmental tolerance. A similar pattern was found in another species trio: allotetraploid Cardamine scutata and its parents. Using the close relatedness of Cardamine and Arabidopsis, we quantified genomewide expression patterns following dry and wet treatments using an Arabidopsis microarray. Hierarchical clustering analysis revealed that the expression pattern of C. flexuosa clustered with C. hirsuta in the dry condition and with C. amara in the wet condition, supporting our hypothesis. Furthermore, the induction levels of most genes in the allopolyploid were lower than in a specialist diploid species. This reflects a disadvantage of being allopolyploid arising from fixed heterozygosity. We propose that recurrent allopolyploid speciation along soil moisture and waterlogging gradients confers niche differentiation and reproductive isolation simultaneously and serves as a model for studying the molecular basis of ecological speciation and adaptive radiation.

Whole genome sequences, which can be provided even for non-model organisms owing to high-throughput sequencers, are valuable in enhancing the understanding of adaptive evolution. Metrosideros polymorpha, a tree species endemic to the Hawaiian Islands, occupies a wide range of ecological habitats and shows remarkable polymorphism in phenotypes among/within populations. The biological functions of genetic variations observed within this species could provide significant insights into the adaptive radiation found in a single species. Here de novo assembled genome sequences of M. polymorpha are presented to reveal basic genomic parameters about this species and to develop our knowledge of ecological divergences. The assembly yielded 304-Mbp genome sequences, half of which were covered by 19 scaffolds with >5 Mbp, and contained 30 K protein-coding genes. Demographic history inferred from the genome-wide heterozygosity indicated that this species experienced a dramatic rise and fall in the effective population size, possibly owing to past geographic or climatic changes in the Hawaiian Islands. This M. polymorpha genome assembly represents a high-quality genome resource useful for future functional analyses of both intra- and interspecies genetic variations or comparative genomics.

Allopolyploids possess complete sets of genomes derived from different parental species and exhibit a range of variation in various traits. Reproductive traits may play a key role in the reproductive isolation between allopolyploids and their parental species, thus affecting the thriving of allopolyploids. However, empirical data, especially in natural habitats, comparing reproductive trait variation between allopolyploids and their parental species remain rare. Here, we documented the flowering phenology and floral morphology of the allopolyploid wild plantCardamine flexuosaand its diploid parentsC. amaraandC. hirsutain their native range in Switzerland. The flowering ofC. flexuosastarted at an intermediate time compared with those of the parents and the flowering period ofC. flexuosaoverlapped with those of the parents.Cardamine flexuosaresembledC. hirsutain the size of flowers and petals and the length/width ratio of petals, while it resembledC. amarain the length/width ratio of flowers. These results provide empirical evidence of the trait-dependent variation of allopolyploid phenotypes in natural habitats at the local scale. They also suggest that the variation in some reproductive traits inC. flexuosais associated with self-fertilization. Therefore, it is helpful to consider the mating system in furthering the understanding of the processes that may have shaped trait variation in polyploids in nature.

Genome duplication is widespread in wild and crop plants. However, little is known about genome-wide selection in polyploids due to the complexity of duplicated genomes. In polyploids, the patterns of purifying selection and adaptive substitutions may be affected by masking owing to duplicated genes or homeologs as well as effective population size. Here, we resequence 25 accessions of the allotetraploid Arabidopsis kamchatica, which is derived from the diploid species A. halleri and A. lyrata. We observe a reduction in purifying selection compared with the parental species. Interestingly, proportions of adaptive non-synonymous substitutions are significantly positive in contrast to most plant species. A recurrent pattern observed in both frequency and divergence–diversity neutrality tests is that the genome-wide distributions of both subgenomes are similar, but the correlation between homeologous pairs is low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation., Nature Communications, 9, ISSN:2041-1723

Pitchers are modified leaves used by carnivorous plants for trapping prey. Their fluids contain digestive enzymes from the plant and they harbor abundant microbes. In this study, the diversity of bacterial communities was assessed in Nepenthes pitcher fluids and the composition of the bacterial community was compared to that in other environments, including the phyllosphere of Arabidopsis, animal guts and another pitcher plant, Sarracenia. Diversity was measured by 454 pyrosequencing of 16S rRNA gene amplicons. A total of 232,823 sequences were obtained after chimera and singleton removal that clustered into 3260 distinct operational taxonomic units (OTUs) (3% dissimilarity), which were taxonomically distributed over 17 phyla, 25 classes, 45 orders, 100 families, and 195 genera. Pyrosequencing and fluorescence in situ hybridization yielded similar estimates of community composition. Most pitchers contained high proportions of unique OTUs, and only 22 OTUs (

Beneficial utilization of yuzu (Citrus junos) peel was investigated to improve the commercial value of cultured yellowtail fish. The antioxidant effects of grated yuzu peel from pomace (yuzu paste) on prevention of dark muscle discoloration during storage in sliced yellowtail fish were tested. Four diets were prepared, containing 0, 10, 50, and 100 g yuzu paste in a 1,450-g diet (wet basis). Fish were fed one of the four diets for 10 weeks. Growth performance was not significantly different among the dietary groups, but fish fed a diet containing 100-g yuzu paste showed the least average body weight and a significant increase in fecal amount and fat levels in the feces, which suggest low digestibility and low absorption. Dark muscle discoloration was significantly reduced in all yuzu dietary groups compared to the control group during storage at 4°C. The optimal supplementation of yuzu paste in the fish diet is very effective at maintaining fish flesh freshness as a finishing diet without causing addition...

This article describes the use of cytogenomic and molecular approaches to explore the origin and evolution of Cardamine schulzii, a textbook example of a recent allopolyploid, in its ;110-year history of human-induced hybridization and allopolyploidy in the Swiss Alps. Triploids are typically viewed as bridges between diploids and tetraploids but rarely as parental genomes of high-level hybrids and polyploids. The genome of the triploid semifertile hybrid Cardamine 3 insueta (2n = 24, RRA) was shown to combine the parental genomes of two diploid (2n =2 x = 16) species, Cardamine amara (AA) and Cardamine rivularis (RR). These parental genomes have remained structurally stable within the triploid genome over the >100 years since its origin. Furthermore, we provide compelling evidence that the alleged recent polyploid C. schulzii is not an autohexaploid derivative of C. 3 insueta. Instead, at least two hybridization events involving C. 3 insueta and the hypotetraploid Cardamine pratensis (PPPP, 2n =4 x22 = 30) have resulted in the origin of the trigenomic hypopentaploid (2n =5 x22 = 38, PPRRA) and hypohexaploid (2n =6 x22 = 46, PPPPRA). These data show that the semifertile triploid hybrid can promote a merger of three different genomes and demonstrate how important it is to reexamine the routinely repeated textbook examples using modern techniques.

We determined the environmental requirements for Lepus brachyurus lyoni on Sado Island, Japan, during the winter when food resources are low. Hare track survey sites were classified by vegetation type. The movement distances of hares, which indicated habitat preference, were evaluated as the relative length of tracks in a 1-ha area. In addition, we examined browse marks on plants and the protein content of plants to determine the preferred plant species. Movement distances of hares decreased significantly with increasing tree stand height, mean tree diameter, basal area of the tree stand, and forest canopy closure, but increased with branch-and-stem density. The percentage of browse marks on the branches of tree/shrub species decreased significantly with increasing branch-and-stem diameter. The rate of feeding increased significantly with increased protein content in the branches. These findings suggest that hares prefer shrub stands with high branch-and-stem density to mature forests, which hav...

We investigated the substrate specificity of farnesyl diphosphate (FPP) synthase derived from Bacillus stearothermophilus and porcine liver by examining the reactivities of two cyclic substrate homologs, cyclohexylideneethyl diphosphate and cyclohexenylethyl diphosphate. Reaction of geranyl diphosphate with 2-cyclohexenylethyl diphosphate using bacterial or porcine liver FPP synthase produced (S)-geranylcyclohexylideneethyl diphosphate, with relative yields of 13.6% for the bacterial enzyme and 42.2% for the porcine liver enzyme. Reaction of cyclohexylideneethyl diphosphate with isopentenyl diphosphate produced 10-cyclohexyliden-3,7-dimethyldeca-2,6-dien-1-ol as a double condensation product, with relative yields of 23.1% (bacterial enzyme) and 3.0% (porcine liver enzyme). Reaction of cyclohexylideneethyl diphosphate with 2-cyclohexenylethyl diphosphate using bacterial enzyme produced (cyclohexylideneethyl)-cyclohexylideneethyl diphosphate (0.8% yield).

We present the technique of instrumental delay calibration for the dual-beam system of VLBI Exploration of Radio Astrometry (VERA), namely, the horn-on-dish method, in which artificial noise sources are mounted on the antenna feedome base and a wide-band radio noise is injected into the dual-beam receivers after reflection by a subreflector. We introduce the basic concept of calibration with the horn-on-dish method, and also present results of the experiments to evaluate its calibration accuracy. Detailed comparisons between model path calculations and measured paths from the noise sources show that the horn-on-dish method can calibrate the dual-beam delay difference in the antenna structure and receiver within an � 0.1 mm level. We estimated that the systematic error in

We observed the SiO (v = 1 and v = 2, J = 1–0) maser emissions toward the Mira variable IK Tauri (IK Tau, NML Tau, IRC +10050) over nine epochs from 2003 November to 2005 April using the VLBI Exploration of Radio Astrometry (VERA) telescope array. We found that the SiO maser distributions around IK Tau are highly variable, depending on the stellar pulsation phase. The velocity structures were complex and also time-variable, and are inconsistent with a simply rotating shell that was suggested by previous observations. Based on fittings of the SiO maser distributions to elliptical ring models, we found that the ring size seems to vary in correlation with the pulsation phase, as previously found for TX Cam. Comparisons of the v = 1 and v = 2 maser distributions reveal that 42–50% of the maser pairs have a positional offset less than 0.5 mas, suggesting that the maser pumping in these spots is likely to be dominated by line overlapping or collisional pumping, rather than pure radiative pumping. In order to model the velocity structure of the spoke-like features observed in IK Tau, we propose a ballistic-orbit model, in which a gas clump ejected from the stellar surface moves radially outward with a gravitational deceleration, and argue that the stellar mass can be deduced from that model.

We report on results of five-epoch VLBI observations of H2O maser emission in the M-type star IRC � 10414, carried out with the VLBI Exploration of Radio Astrometry (VERA). The maser distribution extends over an area of 70 mas � 260 mas and exhibits a bipolar structure. The relative proper motions of 17 maser features were measured during the monitoring observations spanning nine months. The distance to IRC � 10414 was re-estimated on the basis of the statistical treatment of parallax and the model-fitting method, yielding D = 3.1 ˙ 0.4 kpc and D = 2.0 ˙ 0.2 kpc, respectively. The estimated distance, D = 2–3 kpc, is much larger than that previously adopted. The stellar luminosity of IRC � 10414 is also re-estimated to be L� � 9 � 10 4 (D=2 kpc) 2 Lˇ, much brighter by a factor of 10–20 than previously adopted (L� � 10000 Lˇ). The maser motions exhibit not only a spherically expanding flow with a velocity of � 10 (D=2 kpc) km s � 1 , but also a faster bipolar outflow with a major axis in the north–south direction and at a small inclination angle with respect to the celestial sphere. These characteristics of the star and the

The evolution from outcrossing based on self-incompatibility (SI) to a selfing system is one of the most prevalent transitions in flowering plants. It has been suggested that the loss of SI in Arabidopsis thaliana is associated with pseudogene formation at the SCR male component of the S locus. Recent work, however, suggests that alternative alleles with large deletions at the S locus are also present and may be responsible for the evolution of self-compatibility in this species. We demonstrate that most of these deletion alleles are evolutionarily derived from an S haplotype (haplogroups A) that already possessed the SCR pseudogene. This haplotype and its deletion variants are nearly fixed in Europe. Together with previous transgenic data, these results suggest that the pseudogenization of PsiSCR1 gene changed the SI phenotype in the majority of A. thaliana accessions, and was a critical step in the evolution of selfing in this species. Two other haplogroups (B and C) were also identified, the former of which contains a novel and possibly functional SCR allele. In contrast to haplogroups A, these two haplogroups are found primarily in Africa and Asia. These results suggest that self-compatibility, which appears to be fixed in this species, arose multiple times with different genetic bases, and indicates that a species-specific trait is associated with parallel evolution at the molecular level.

We report on results of multi-epoch VLBI observations of H2O masers associated with a low-mass young stellar object, IRAS 16293 2422 in Oph East, and a fringe-phase and position reference source, ICRF J162546.8 252738, using the VLBI Exploration of Radio Astrometry (VERA) for high-precision astrometry. We obtained an annual parallax of a maser feature to be = 5.6 0:5 mas, corresponding to a distance of D= 178 +18 37 pc. We also found 10 relative proper motions of maser features with respect to the maser feature mentioned above. The motion of the accompanying young stellar object (YSO) has already been found in thermal continuum emission previously observed with the Very Large Array. The intrinsic motions of masers have been estimated from the relative proper motions after the YSO’s motion is subtracted from, and a systemic secular motion of the position reference feature is added to the proper motions originally measured. The intrinsic maser kinematical structure may trace a bipolar outflow.

53歳，男性。初診の約3週間前より両手指から手背にかけて，疼痛・しびれを伴う浮腫が出現し，左第1指から第3指にかけては紫紅色調の紅斑も伴っていた。これらの症状は消炎鎮痛薬内服，ステロイド外用では改善しなかった。当科初診時，末梢血好酸球増多(1748/μl)があり，皮膚所見と合わせ，episodic angioedema with eosinophiliaを疑った。ところが加療中も，足背浮腫や，右示指に冷感を伴ったチアノーゼ，網状皮斑が出現し，さらには血痰も伴うようになった。再検したところ，好酸球増多は進行し(7951/μl)，血管内播種性凝固症候群(DIC)を伴っていることが判明した。好酸球増多について骨髄検査を含めて精査を行ったが明らかな異常はなく，最終的にhypereosinophilic syndrome(HES)と診断した。治療はHESに対してpredonisolone 60mg，DICに対してgabexate mesilateで治療を開始し，軽快した。初診時でのHES の診断は困難であるが，本症例のように非典型的な手の浮腫を認めた場合にはHESも含めた鑑別を挙げる必要があると考えられた。

Genomewide markers enable us to study genetic differentiation within a species and the factors underlying it at a much higher resolution than before, which advances our understanding of adaptation in organisms. We investigated genomic divergence in Metrosideros polymorpha, a woody species that occupies a wide range of ecological habitats across the Hawaiian Islands and shows remarkable phenotypic variation. Using 1659 single nucleotide polymorphism (SNP) markers annotated with the genome assembly, we examined the population genetic structure and demographic history of nine populations across five elevations and two ages of substrates on Mauna Loa, the island of Hawaii. The nine populations were differentiated into two genetic clusters distributed on the lower and higher elevations and were largely admixed on the middle elevation. Demographic modelling revealed that the two genetic clusters have been maintained in the face of gene flow, and the effective population size of the high-altitude cluster was much smaller. A FST -based outlier search among the 1659 SNPs revealed that 34 SNPs (2.05%) were likely to be under divergent selection and the allele frequencies of 21 of them were associated with environmental changes along elevations, such as temperature and precipitation. This study shows a genomic mosaic of M. polymorpha, in which contrasting divergence patterns were found. While most genomic polymorphisms were shared among populations, a small fraction of the genome was significantly differentiated between populations in diverse environments and could be responsible for the dramatic adaptation to a wide range of environments.

Ralstonia eutropha is a facultative chemolithoautotrophic bacterium that uses the Calvin–Benson–Bassham (CBB) cycle for CO2 fixation. This study showed that R. eutropha strain H16G incorporated 13CO2, emitted by the oxidative decarboxylation of [1-13C1]-glucose, into key metabolites of the CBB cycle and finally into poly(3-hydroxybutyrate) [P(3HB)] with up to 5.6% 13C abundance. The carbon yield of P(3HB) produced from glucose by the strain H16G was 1.2 times higher than that by the CBB cycle-inactivated mutants, in agreement with the possible fixation of CO2 estimated from the balance of energy and reducing equivalents through sugar degradation integrated with the CBB cycle. The results proved that the ‘gratuitously’ functional CBB cycle in R. eutropha under aerobic heterotrophic conditions participated in the reutilization of CO2 emitted during sugar degradation, leading to an advantage expressed as increased carbon yield of the storage compound. This is a new insight into the role of the CBB cycle and may be applicable for more efficient utilization of biomass resources.

To evaluate the effect of low-molecular-weight glutenin subunit (LMW-GS) genes on dough strength, locus-specific primers of LMW-GS genes and gliadin bands tightly linked to LMW-GS genes were analyzed in common wheat. Segregation analysis of the F2 progeny from a cross between ‘Haruhikari’, a good bread-making quality cultivar, and ‘Asakaze-komugi’, a poor bread-making quality cultivar, showed that dough strength significantly correlated with one amplified LMW-GS gene located at the Glu-B3 locus from ‘Haruhikari’. There was no specific reference to the gliadin bands identified as promising markers in the cross under study. The LMW-GS gene of ‘Haruhikari’ had a seven amino-acid deletion in the repetitive domain relative to ‘Asakaze-komugi’, as well as six amino-acid substitutions, three of which would be expected to cause changes in hydrophilicity. The presence of the LMW-GS gene and other LMW-GS genes tightly linked to it may affect the dough strength of wheat.

In magnesia cement, phase 3, a broad and strong infrared band was observed with the maximum at ∼1300 and 1050 cm −1 in the H and D systems, respectively. To clarify the origin of the 1300 cm −1 band the temperature dependency of the infrared spectra of the H system was observed and the spectra analyzed on the basis of a strong vibrational coupling of the OH stretching with lattice modes. The fitting was quite well, giving rise to the origin of the 1300 cm −1 band of the OH stretching.

The theoretical study on the mechanism of butane oxidation using model complexes of vanadyl pyrophosphate has been investigated using density functional theory (DFT) method. The monomeric complex VO(OH) 2 (OH 2 ) 2 was selected as a fundamental structure. The complexes bearing one phosphoric residue were selected for clarifying the effect of pyrophosphoric moieties on the catalyst. The complexes having two vanadium units were selected as two-layer models of the catalyst for clarifying the influence of the presence or absence of lattice oxygen and the effect of the oxidation states of the inner vanadium atom. The introduction of a phosphoric moiety on one of the hydroxy groups strongly stabilizes the lower oxidation states of the complexes. This result suggests that the surface vanadium species having the higher 5+ oxidation state should possess stronger oxidation ability. The presence of the vanadium (4+) atom at the lower layer relatively destabilizes the V 3+ state of the upper vanadium complexes, and stabilizes the peroxo-vanadium (4+) complexes, which suggests that the lattice oxo-oxygen in vanadyl pyrophosphate may play an important role in the activation of molecular oxygen.

Introduction of fluorine atom(s) at the γ- and δ-positions of alkyl iodides increased the selectivities toward palladium-catalyzed cross-coupling reaction with organostannanes. A similar effect of fluorine substituents on the selectivities was also observed in the palladium-catalyzed carbonylative coupling reaction of alkyl iodides with phenyltributyltin under CO pressure.

Branchio-oto (BO) syndrome is complicated with congenital preauricular fistulae, branchial fistulae (cysts), and hearing loss (sensorineural, conductive or mixed). As well as branchio-oto-renal (BOR) syndrome, it is known to be an autosomal dominant hereditary disorder. Since mutations in the EYA1 gene have been identified in both BO and BOR syndromes, mutation screening of this gene has been drawing attention as a genetic test to diagnose BOR/BO syndromes. In this study, we genetically investigated the presence of EYA1 mutations in a BO syndrome family in which we observed congenital preauricular fistulae, branchial fistulae (cysts) and hearing loss in four generations. Whereas there was a variety of phenotype expressions in this family, all subjects tested had a nonsense mutation (R264X) in exon 8 of the EYA1 gene. The present report adds further examples to support the usefulness of molecular genetic testing for the diagnosis of patients with BO syndrome.

β-Perfluoroalkyl-substituted alkyl halides reacted with organostamnanes such as allylphenylethynyl-, β-phenylethenyl-, and phenyl-tributyltin in the presence of palladium-phosphine complexes to give the corresponding cross-coupling products in good yields. When the reaction was carried out under CO pressure, carbonylative coupling of the halides took place affording the corresponding fluorine-contaming ketones in good yields.

Coupling reaction of β-perfluoroalkyl-substituted alkyl halides with Grignard reagents such as phenyl-, vinyl-, allyl-, benzyl-, and alkyl-magnesium halides was catalyzed by copper salts or complexes to give the corresponding cross-coupling products in good yields. α,ω-Diiodoalkane bearing a polyfluoroalkylene moiety also reacted with 2 equiv. of Grignard reagent in the presence of copper catalyst to give α,ω-bi-functionalized product.

Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

Coupling reaction of β-perfluoroalkyl-substituted alkyl halides with Grignard reagents such as phenyl-, vinyl-, allyl-, benzyl-, and alkyl-magnesium halides was catalyzed by copper salts or complexes to give the corresponding cross-coupling products in good yields. α,ω-Diiodoalkane bearing a polyfluoroalkylene moiety also reacted with 2 equiv. of Grignard reagent in the presence of copper catalyst to give α,ω-bi-functionalized product.

β-Perfluoroalkyl-substituted alkyl halides reacted with organostamnanes such as allylphenylethynyl-, β-phenylethenyl-, and phenyl-tributyltin in the presence of palladium-phosphine complexes to give the corresponding cross-coupling products in good yields. When the reaction was carried out under CO pressure, carbonylative coupling of the halides took place affording the corresponding fluorine-contaming ketones in good yields.