Search

Hibiscus trionum, commonly known as the ’Flower of an Hour’, is an easily cultivated plant in the Malvaceae family. The purple base part of its petal exhibits structural color due to the fine ridges on the epidermal cell surface, and the molecular mechanism of ridge formation has been actively investigated. We performed genome sequencing ofH. trionumusing a long-read sequencing technology with transcriptome and pathway analyses to identify candidate genes for fine structure formation. The ortholog ofAtSHINE1, which is involved in the biosynthesis of cuticular wax inArabidopsis thaliana, was significantly overexpressed in the iridescent tissue. In addition, orthologs ofAtCUS2andAtCYP77A, which contribute to cutin synthesis, were also overexpressed. Our results provide important insights into the formation of fine ridges on epidermal cells in plants usingH. trionumas a model.

The microbiome of plants plays a pivotal role in their growth and health. Despite its importance, many fundamental questions about the microbiome remain largely unanswered, such as the identification of colonizing bacterial species, the genes they carry, and the location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice leaf microbiome, we performed a metagenomic analysis using long-read sequences, and developed a genomic DNA extraction method that provides relatively intact DNA for long-read sequencing. 1.8 Gb reads were assembled into 26,067 contigs, including 136 circular sequences of less than 1 Mbp, as well as 172 large (≥ 1 Mbp) sequences, six of which were circularized. Within these contigs, 669 complete 16S rRNA genes were clustered into 166 bacterial species, 130 of which showed low identity to previously defined sequences, suggesting that they represent novel species. The large circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs (Candidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies.

NHK’s morning dramas, commonly known as asadora, usually focus on the lives of female heroines who cheerfully persevere in the face of adversity. They depict how women have responded to changing times, especially during and after the Asia-Pacific War. Since 2010, asadora have achieved increased popularity, and many of the shows broadcast since 2011 – the year of the Great East Japan Earthquake – have returned to the traditional theme of women during war. This study investigates asadora that depict the war period, focusing on the representation of 15 August 1945 since the format’s earliest days in the 1960s. As this study of 15 August scenes in asadora shows, memory of the Asia-Pacific War in Japan changed considerably after the catastrophe of 3/11. By understanding the mechanisms of presenting this specific event in popular media, it is also possible to shed light on the general practices of collective memory in Japan.

Legume plants form a root-nodule symbiosis with rhizobia. This symbiosis establishment generally relies on rhizobium-produced Nod factors (NFs) and their perception by leguminous receptors (NFRs) that trigger nodulation. However, certain rhizobia hijack leguminous nodulation signalling via their type III secretion system, which functions in pathogenic bacteria to deliver effector proteins into host cells. Here, we report that rhizobia use pathogenic-like effectors to hijack legume nodulation signalling. The rhizobial effector Bel2-5 resembles the XopD effector of the plant pathogen Xanthomonas campestris and could induce nitrogen-fixing nodules on soybean nfr mutant. The soybean root transcriptome revealed that Bel2-5 induces expression of cytokinin-related genes, which are important for nodule organogenesis and represses ethylene- and defense-related genes that are deleterious to nodulation. Remarkably, Bel2-5 introduction into a strain unable to nodulate soybean mutant affected in NF perception conferred nodulation ability. Our findings show that rhizobia employ and have customized pathogenic effectors to promote leguminous nodulation signalling.

Nitrogen deficiency affects soybean growth and physiology, such as symbiosis with rhizobia; however, its effects on the bacterial composition of the soybean root microbiota remain unclear. A bacterial community analysis by 16S rRNA gene amplicon sequencing showed nitrogen deficiency-induced bacterial community shifts in soybean roots with the marked enrichment of Methylobacteriaceae. The abundance of Methylobacteriaceae was low in the roots of field-grown soybean without symptoms of nitrogen deficiency. Although Methylobacteriaceae isolated from soybean roots under nitrogen deficiency did not promote growth or nodulation when inoculated into soybean roots, these results indicate that the enrichment of Methylobacteriaceae in soybean roots is triggered by nitrogen-deficiency stress.

Pseudomonas amygdali pv. tabaci strain 6605 is the bacterial pathogen causing tobacco wildfire disease that has been used as a model for elucidating virulence mechanisms. Here, we present the complete genome sequence of P. amygdali pv. tabaci 6605 as a circular chromosome from reads using a PacBio sequencer.

Plant roots constitute the primary interface between plants and soilborne microorganisms and harbor microbial communities called the root microbiota. Recent studies have demonstrated a significant contribution of plant specialized metabolites (PSMs) to the assembly of root microbiota. However, the mechanistic and evolutionary details underlying the PSM-mediated microbiota assembly and its contribution to host specificity remain elusive. Here, we show that the bacterial genus Arthrobacter is predominant specifically in the tobacco endosphere and that its enrichment in the tobacco endosphere is partially mediated by a combination of two unrelated classes of tobacco-specific PSMs, santhopine and nicotine. We isolated and sequenced Arthrobacter strains from tobacco roots as well as soils treated with these PSMs and identified genomic features, including but not limited to genes for santhopine and nicotine catabolism, that are associated with the ability to colonize tobacco roots. Phylogenomic and comparative analyses suggest that these genes were gained in multiple independent acquisition events, each of which was possibly triggered by adaptation to particular soil environments. Taken together, our findings illustrate a cooperative role of a combination of PSMs in mediating plant species-specific root bacterial microbiota assembly and suggest that the observed interaction between tobacco and Arthrobacter may be a consequence of an ecological fitting process. IMPORTANCE Host secondary metabolites have a crucial effect on the taxonomic composition of its associated microbiota. It is estimated that a single plant species produces hundreds of secondary metabolites; however, whether different classes of metabolites have distinctive or common roles in the microbiota assembly remains unclear. Here, we show that two unrelated classes of secondary metabolites in tobacco play a cooperative role in the formation of tobacco-specific compositions of the root bacterial microbiota, which has been established as a consequence of independent evolutionary events in plants and bacteria triggered by different ecological effects. Our findings illustrate mechanistic and evolutionary aspects of the microbiota assembly that are mediated by an arsenal of plant secondary metabolites.

Plant roots constitute the primary interface between plants and soilborne microorganisms and harbor microbial communities called the root microbiota. Recent studies have demonstrated a significant contribution of plant specialized metabolites (PSMs) to the assembly of root microbiota. However, the mechanistic and evolutionary details underlying the PSM-mediated microbiota assembly and its contribution to host specificity remain elusive. Here, we show that the bacterial genus Arthrobacter is predominant specifically in the tobacco endosphere and that its enrichment in the tobacco endosphere is partially mediated by a combination of two unrelated classes of tobacco-specific PSMs, santhopine and nicotine. We isolated and sequenced Arthrobacter strains from tobacco roots as well as soils treated with these PSMs and identified genomic features, including but not limited to genes for santhopine and nicotine catabolism, that are associated with the ability to colonize tobacco roots. Phylogenomic and comparative analyses suggest that these genes were gained in multiple independent acquisition events, each of which was possibly triggered by adaptation to particular soil environments. Taken together, our findings illustrate a cooperative role of a combination of PSMs in mediating plant species-specific root bacterial microbiota assembly and suggest that the observed interaction between tobacco and Arthrobacter may be a consequence of an ecological fitting process.

The timing of market entry for generic drugs or biosimilars based on patent expiration is not always clear for producers of generic drugs and biosimilars or brand-name drug companies, because of an uncertainty due to patent infringement, the market environment, and legislation. In Japan, the policy of promoting the use of generic drugs began in the early 2000s, and the government’s target for generic drug use rate is 80% by 2020. In addition to this drastic change in the market environment, changes in legislation have complicated the timing of market entry for generic drugs and biosimilars. Although there is a relatively low number of patent infringement lawsuits filed against producers of generic drugs and biosimilars each year, emerging litigation issues are likely influenced by recent changes in the market environment and legislation. This article provides an overview of recent legislative changes, analyzes the trends in patent infringement litigation, and discusses litigation issues related to the stable supply of generic drugs and biosimilars in Japan. In light of the emerging issues in this field, producers of generic drugs and biosimilars will require more diligence to avoid patent infringement, and institutional reforms are suggested to reduce an increase in patent infringement litigation.

Members of the Colletotrichum gloeosporioides species complex are causal agents of anthracnose in many commercially important plants. Closely related strains have different levels of pathogenicity on hosts despite their close phylogenetic relationship. To gain insight into the genetics underlying these differences, we generated and annotated whole-genome assemblies of multiple isolates of C. fructicola (Cf) and C. siamense (Cs), as well as three previously unsequenced species, C. aenigma (Ca), C. tropicale and C. viniferum with different pathogenicity on strawberry. Based on comparative genomics, we identified accessory regions with a high degree of conservation in strawberry-pathogenic Cf, Cs and Ca strains. These regions encode homologs of pathogenicity-related genes known as effectors, organized in syntenic gene clusters, with copy number variations in different strains of Cf, Cs and Ca. Analysis of highly contiguous assemblies of Cf, Cs and Ca revealed the association of related accessory effector gene clusters with telomeres and repeat-rich chromosomes and provided evidence of exchange between these two genomic compartments. In addition, expression analysis indicated that orthologs in syntenic gene clusters showed a tendency for correlated gene expression during infection. These data provide insight into mechanisms by which Colletotrichum genomes evolve, acquire and organize effectors. This article is protected by copyright. All rights reserved.

Plant specialized metabolites (PSMs) influence the taxonomic compositions of the root-associated microbiota; however, the underlying molecular mechanisms and evolutionary trajectories remain elusive. Here, we show that the bacterial genus Arthrobacter is predominant in the tobacco endosphere, and that its enrichment is mediated by a combination of two tobacco-specific PSMs, santhopine and nicotine The isolation and whole genome sequencing of a representative set of Arthrobacter strains identified independent genomic features, including but not limited to genes for santhopine and nicotine catabolism, which are associated with the colonization competence of tobacco roots. Taken together, these data suggest that plant species-specific root microbiota assembly is mediated by bacterial catabolism of a cocktail of PSMs synthesized by the host plant.

Members of theColletotrichum gloeosporioidesspecies complex are causal agents of anthracnose in a wide range of commercially important plants. To provide an in-depth overview of its diversity, we sequenced the genomes of fungi belonging to this group, including multiple strains ofC. fructicola(Cf) andC. siamense(Cs), as well as representatives of three previously unsequenced species,C. aenigma(Ca),C. tropicaleandC. viniferum. Comparisons between multipleCfandCsstrains led to the identification of accessory regions that show variable conservation in both lineages. These accessory regions encode effector candidate genes, including homologs of previously characterized effectors, organized in clusters of conserved synteny with copy number variations in different strains ofCf, CsandCa. Analysis of highly contiguous assemblies ofCf, CsandCastrains revealed the association of such accessory effector gene clusters with subtelomeric regions and repeat-rich minichromosomes and provided evidence of gene transfer between these two genomic compartments. In addition, expression analysis indicated that paralogs associated with clusters of conserved synteny showed a tendency for correlated gene expression. These data highlight the importance of subtelomeric regions and repeat-rich chromosomes to the genome plasticity ofColletotrichumfungi.

Azospirillum sp. strain B510 has been known as the plant growth-promoting endophyte; however, the growth-promotion effect is dependent on the plant genotype. Here, we aimed to identify quantitative trait loci (QTL) related to primary root length in rice at the seedling stage as a response to inoculation with B510. The primary root length of “Nipponbare” was significantly reduced by inoculation with B510, whereas that of “Kasalath” was not affected. Thus, we examined 98 backcrossed inbred lines and four chromosome segment substitution lines (CSSL) derived from a cross between Nipponbare and Kasalath. The primary root length was measured as a response to inoculation with B510, and the relative root length (RRL) was calculated based on the response to non-inoculation. Three QTL alleles, qRLI-6 and qRLC-6 on Chromosome (Chr.) 6 and qRRL-7 on Chr. 7 derived from Kasalath increased primary root length with inoculation (RLI), without inoculation, (RLC) and RRL and explained 20.2%, 21.3%, and 11.9% of the phenotypic variation, respectively. CSSL33, in which substitution occurred in the vicinity region of qRRL-7, showed a completely different response to inoculation with B510 compared with Nipponbare. Therefore, we suggest that qRRL-7 might strongly control root growth in response to inoculation with Azospirillum sp. strain B510.

A patient organization was founded in 2013 due to skepticism about the safety of human papilloma virus (HPV) vaccines. To evaluate the impact of “priming” patients with information on adverse events following immunization (AEFI) via mainstream media and its impact on reporting by marketing authorization holders (MAHs), healthcare professionals (HCPs), and patients, and to assess the contribution of a pilot patient reporting system for adverse events in Japan to pharmacovigilance. A summary list of reports of anaphylaxis, vagal reflex, and generalized pain-related AEFI, as presented to the Vaccine Adverse Reactions Review Committee (VARRC) between 2011 and 2016, was analyzed to gain information on MAH and HCP reports. Data on patient AEFI reporting were obtained from a pilot Pharmaceuticals and Medical Devices Agency (PMDA) database designed for this purpose. Data on vaccine shipment volumes were obtained from the VARRC. The leading reporting source transitioned from MAHs (82% of the total AEFI reported in 2010) to HCPs (63% in 2011), and patients (43% in 2015). Sharp peaks were observed for both MAH and HCP reports in 2011. A second peak in pain-related AEFIs reported by HCPs was observed in 2013 when the Ministry of Health, Labour and Welfare suspended the active recommendation of HPV vaccines. Patient reports were continuous and accounted for 21.7% of the total AEFIs reported to the current patient reporting system. In Japan, the characteristics of AEFI reports differed by source for HPV vaccines. MAH and HCP reports identified the major trend in AEFI occurrence during the early post-marketing phase, whereas patient reports in cooperation with HCPs facilitated the detection of weak signals of possible AEFIs throughout the product lifecycle. Patient reporting systems should be encouraged, especially by promoting the communication between patients and local “home” pharmacies in cooperation with patient organizations.

Fusarium oxysporum f. sp. cubense is the causal agent of banana Fusarium wilt, also known as Panama disease. Here, we present a high-quality genome sequence of F. oxysporum f. sp. cubense strain 160527. The genome assembly is composed of 12 contigs with a total assembly length of 51,139,495 bp (N50 contig length, 4,884,632 bp).

Symbiosis between legumes and rhizobia leads to the formation of N2-fixing root nodules. In soybean, several host genes, referred to as Rj genes, control nodulation. Soybean cultivars carrying the Rj4 gene restrict nodulation by specific rhizobia such as Bradyrhizobium elkanii We previously reported that the restriction of nodulation was caused by B. elkanii possessing a functional type III secretion system (T3SS), which is known for its delivery of virulence factors by pathogenic bacteria. In the present study, we investigated the molecular basis for the T3SS-dependent nodulation restriction in Rj4 soybean. Inoculation tests revealed that soybean cultivar BARC-2 (Rj4/Rj4) restricted nodulation by B. elkanii USDA61, whereas its nearly isogenic line BARC-3 (rj4/rj4) formed nitrogen-fixing nodules with the same strain. Root-hair curling and infection threads were not observed in the roots of BARC-2 inoculated with USDA61, indicating that Rj4 blocked B. elkanii infection in the early stages. Accumulation of H2O2 and salicylic acid (SA) was observed in the roots of BARC-2 inoculated with USDA61. Transcriptome analyses revealed that inoculation of USDA61, but not its T3SS mutant in BARC-2, induced defense-related genes, including those coding for hypersensitive-induced responsive protein, which act in effector-triggered immunity (ETI) in Arabidopsis. These findings suggest that B. elkanii T3SS triggers the SA-mediated ETI-type response in Rj4 soybean, which consequently blocks symbiotic interactions. This study revealed a common molecular mechanism underlying both plant-pathogen and plant-symbiont interactions, and suggests that establishment of a root nodule symbiosis requires the evasion or suppression of plant immune responses triggered by rhizobial effectors.

Under paddy field conditions, biological sulfur oxidation occurs in the oxidized surface soil layer and rhizosphere, in which oxygen leaks from the aerenchyma system of rice plants. In the present study, we examined community shifts in sulfur-oxidizing bacteria associated with the oxidized surface soil layer and rice roots under different sulfur fertilization conditions based on the 16S ribosomal RNA (rRNA) gene in order to explore the existence of oligotrophic sulfur-oxidizing bacteria in the paddy rice ecosystem. Rice plants were grown in pots with no fertilization (control) or CaCO3 or CaSO4 fertilization. A principal-coordinates analysis (PCoA) showed that CaSO4 fertilization markedly affected bacterial communities associated with rice roots and soil, whereas no significant differences were observed in plant growth among the fertilizer treatments examined. In rice roots, the relative abundance of Acidobacteria, Alphaproteobacteria, Gammaproteobacteria, and TM7 was significantly higher in CaSO4-fertilized pots than in control pots. Alphaproteobacteria, Bradyrhizobiaceae, and Methylocystaceae members were significantly more abundant in CaSO4-fertilized roots than in control roots. On the other hand, the abundance of Actinobacteria and Proteobacteria was lower in CaSO4-fertilized soil than in control soil. These results indicate that the bacteria associated with rice roots and soil responded to the sulfur amendment, suggesting that more diverse bacteria are involved in sulfur oxidation in the rice paddy ecosystem than previously considered.

Methylobacterium species are representative of methylotrophic bacteria. Their genomes usually encode two types of methanol dehydrogenases (MDHs): MxaF and XoxF. The former is a Ca 2+ -dependent enzyme, and the latter was recently determined to be a lanthanide-dependent enzyme that is necessary for the expression of mxaF . This finding revealed the unexpected and important roles of lanthanides in bacterial methylotrophy. In this study, we performed transcriptome sequencing (RNA-seq) analysis using M. aquaticum strain 22A grown in the presence of different lanthanides. Expression of mxaF and xoxF1 genes showed a clear inverse correlation in response to La 3+ . We observed downregulation of formaldehyde oxidation pathways, high formaldehyde dehydrogenase activity, and low accumulation of formaldehyde in the reaction with cells grown in the presence of La 3+ ; this might be due to the direct oxidation of methanol to formate by XoxF1. Lanthanides induced the transcription of AT-rich genes, the function of most of which was unknown, and genes possibly related to cellular survival, as well as other MDH homologues. These results revealed not only the metabolic response toward altered primary methanol oxidation, but also the possible targets to be investigated further in order to better understand methylotrophy in the presence of lanthanides. IMPORTANCE Lanthanides have been considered unimportant for biological processes. In methylotrophic bacteria, however, a methanol dehydrogenase (MDH) encoded by xoxF was recently found to be lanthanide dependent, while the classic-type mxaFI is calcium dependent. XoxF-type MDHs are more widespread in diverse bacterial genera, suggesting their importance for methylotrophy. Methylobacterium species, representative methylotrophic and predominating alphaproteobacteria in the phyllosphere, contain both types and regulate their expression depending on the availability of lanthanides. RNA-seq analysis showed that the regulation takes place not only for MDH genes but also the subsequent formaldehyde oxidation pathways and respiratory chain, which might be due to the direct oxidation of methanol to formate by XoxF. In addition, a considerable number of genes of unknown function, including AT-rich genes, were found to be upregulated in the presence of lanthanides. This study provides first insights into the specific reaction of methylotrophic bacteria to the presence of lanthanides, emphasizing the biological relevance of this trace metal.

One of the many disparate lifestyles of Bradyrhizobium diazoefficiens is chemolithotrophic growth with thiosulfate as an electron donor for respiration. The employed carbon source may be CO2 (autotrophy) or an organic compound such as succinate (mixotrophy). Here, we discovered three new facets of this capacity: (i) When thiosulfate and succinate were consumed concomitantly in conditions of mixotrophy, even a high molar excess of succinate did not exert efficient catabolite repression over the use of thiosulfate. (ii) Using appropriate cytochrome mutants, we found that electrons derived from thiosulfate during chemolithoautotrophic growth are preferentially channeled via cytochrome c550 to the aa3-type heme-copper cytochrome oxidase. (iii) Three genetic regulators were identified to act at least partially in the expression control of genes for chemolithoautotrophic thiosulfate oxidation: RegR and CbbR as activators, and SoxR as a repressor.

Lanthanides have been considered unimportant for biological processes. In methylotrophic bacteria, however, a methanol dehydrogenase (MDH) encoded by xoxF was recently found to be lanthanide dependent, while the classic-type mxaFI is calcium dependent. XoxF-type MDHs are more widespread in diverse bacterial genera, suggesting their importance for methylotrophy. Methylobacterium species, representative methylotrophic and predominating alphaproteobacteria in the phyllosphere, contain both types and regulate their expression depending on the availability of lanthanides. RNA-seq analysis showed that the regulation takes place not only for MDH genes but also the subsequent formaldehyde oxidation pathways and respiratory chain, which might be due to the direct oxidation of methanol to formate by XoxF. In addition, a considerable number of genes of unknown function, including AT-rich genes, were found to be upregulated in the presence of lanthanides. This study provides first insights into the specific reaction of methylotrophic bacteria to the presence of lanthanides, emphasizing the biological relevance of this trace metal., Methylobacterium species are representative of methylotrophic bacteria. Their genomes usually encode two types of methanol dehydrogenases (MDHs): MxaF and XoxF. The former is a Ca2+-dependent enzyme, and the latter was recently determined to be a lanthanide-dependent enzyme that is necessary for the expression of mxaF. This finding revealed the unexpected and important roles of lanthanides in bacterial methylotrophy. In this study, we performed transcriptome sequencing (RNA-seq) analysis using M. aquaticum strain 22A grown in the presence of different lanthanides. Expression of mxaF and xoxF1 genes showed a clear inverse correlation in response to La3+. We observed downregulation of formaldehyde oxidation pathways, high formaldehyde dehydrogenase activity, and low accumulation of formaldehyde in the reaction with cells grown in the presence of La3+; this might be due to the direct oxidation of methanol to formate by XoxF1. Lanthanides induced the transcription of AT-rich genes, the function of most of which was unknown, and genes possibly related to cellular survival, as well as other MDH homologues. These results revealed not only the metabolic response toward altered primary methanol oxidation, but also the possible targets to be investigated further in order to better understand methylotrophy in the presence of lanthanides. IMPORTANCE Lanthanides have been considered unimportant for biological processes. In methylotrophic bacteria, however, a methanol dehydrogenase (MDH) encoded by xoxF was recently found to be lanthanide dependent, while the classic-type mxaFI is calcium dependent. XoxF-type MDHs are more widespread in diverse bacterial genera, suggesting their importance for methylotrophy. Methylobacterium species, representative methylotrophic and predominating alphaproteobacteria in the phyllosphere, contain both types and regulate their expression depending on the availability of lanthanides. RNA-seq analysis showed that the regulation takes place not only for MDH genes but also the subsequent formaldehyde oxidation pathways and respiratory chain, which might be due to the direct oxidation of methanol to formate by XoxF. In addition, a considerable number of genes of unknown function, including AT-rich genes, were found to be upregulated in the presence of lanthanides. This study provides first insights into the specific reaction of methylotrophic bacteria to the presence of lanthanides, emphasizing the biological relevance of this trace metal.

Background The aim of the study was to investigate trends in cancer prognosis by examining the relationship between period of diagnosis and probability of death from cancer in a population-based cohort. Methods Within a cohort of Japanese men and women aged 40–69 years and free of prior diagnosis of cancer and cardiovascular disease at baseline, data from 4403 patients diagnosed with cancer between 1990 and 2006 and followed up until 2012 were analyzed using survival regression models to assess the presence of an effect of the period of diagnosis (before 1998 versus after 1998) on the risk of dying from cancer. Results We noted a significant decrease in risk of dying from cancer among individuals diagnosed after 1998 with lung cancer (hazard ratio [HR] = 0.676 [0.571–0.800]) or colorectal cancer (HR = 0.801 [0.661–0.970]). A decrease in the estimated five-year probability of death from cancer was also noted between the first (before 1998) and the second (after 1998) period of diagnosis for lung and colorectal cancers (e.g., 85.4% vs. 73.3% for lung cancer and 44.6% vs. 37.7% for colorectal cancer, respectively, for stage III in men aged 60 at diagnosis). Conclusions This study presented the first scientific evidence of improvement in prognosis for lung and colorectal cancer patients in a population-based cohort in Japan. Our results suggest that recent advances in cancer treatment could have influenced cancer survival differently among lung, colorectal and gastric cancers.

The hydrogen uptake (Hup) system of Bradyrhizobium diazoefficiens recycles the H2 released by nitrogenase in soybean nodule symbiosis, and is responsible for H2-dependent chemolithoautotrophic growth. The strain USDA110 has two hup gene clusters located outside (locus I) and inside (locus II) a symbiosis island. Bacterial growth under H2-dependent chemolithoautotrophic conditions was markedly weaker and H2 production by soybean nodules was markedly stronger for the mutant of hup locus I (ΔhupS1L1) than for the mutant of hup locus II (ΔhupS2L2). These results indicate that locus I is primarily responsible for Hup activity.

Streptococcus intermedius is a known human pathogen and belongs to the anginosus group ( S. anginosus , S. intermedius , and S. constellatus ) of streptococci (AGS). We found a large open reading frame (6,708 bp) in the lac operon, and bioinformatic analysis suggested that this gene encodes a novel glycosidase that can exhibit β- d -galactosidase and N -acetyl-β- d -hexosaminidase activities. We, therefore, named this protein “multisubstrate glycosidase A” (MsgA). To test whether MsgA has these glycosidase activities, the msgA gene was disrupted in S. intermedius . The msgA -deficient mutant no longer showed cell- and supernatant-associated β- d -galactosidase, β- d -fucosidase, N -acetyl-β- d -glucosaminidase, and N -acetyl-β- d -galactosaminidase activities, and all phenotypes were complemented in trans with a recombinant plasmid carrying msgA . Purified MsgA had all four of these glycosidase activities and exhibited the lowest K m with 4-methylumbelliferyl-linked N -acetyl-β- d -glucosaminide and the highest k cat with 4-methylumbelliferyl-linked β- d -galactopyranoside. In addition, the purified LacZ domain of MsgA had β- d -galactosidase and β- d -fucosidase activities, and the GH20 domain exhibited both N -acetyl-β- d -glucosaminidase and N -acetyl-β- d -galactosaminidase activities. The β- d -galactosidase and β- d -fucosidase activities of MsgA are thermolabile, and the optimal temperature of the reaction was 40°C, whereas almost all enzymatic activities disappeared at 49°C. The optimal temperatures for the N -acetyl-β- d -glucosaminidase and N -acetyl-β- d -galactosaminidase activities were 58 and 55°C, respectively. The requirement of sialidase treatment to remove sialic acid residues of the glycan branch end for glycan degradation by MsgA on human α 1 -antitrypsin indicates that MsgA has exoglycosidase activities. MsgA and sialidase might have an important function in the production and utilization of monosaccharides from oligosaccharides, such as glycans for survival in a normal habitat and for pathogenicity of S. intermedius .

Scholarly attention to pharmaceutical companies' ability to sustain research and development (R&D) productivity has increased as they increasingly handle business challenges. Furthermore, the deterioration of R&D productivity has long been considered a major cause of mergers and acquisitions (M&As). This study attempts to investigate quantitatively the possible causes of the deterioration and the relationship between the deterioration and M&As by examining the Japanese pharmaceutical industry. Japan from 1980 to 1997 is an ideal case because of the availability of official data, but more importantly the significant changes in its business environment at the time. Using the Malmquist Index and data envelopment analysis, we measured the deterioration of R&D productivity from 1980 to 1997 based on a sample of 15 Japanese companies. Two lessons can be learned from Japan's case. First, to sustain R&D productivity over the long term, companies should use licensing activities and focus on the dominant therapeutic franchises. Second, if a company fails significantly to catch up with the benchmark, it is likely to pursue an M&A or seek an alternative way to improve R&D productivity. These findings appear similar to the current situation of the global pharmaceutical industry, although Japan pursued more licensing activities than M&A to improve R&D productivity.

WOS: 000399232900008 PubMed ID: 27902265 A novel facultatively methanol-utilizing bacterial strain, SM30(T), was isolated from rice rhizosphere. Strain SM30(T) was Gram-stain-negative, aerobic, motile, short rods, and grew optimally at pH 7 and at 28 degrees C. It could tolerate 0 to 2%(w/v) NaCl. Based on 16S rRNA gene sequence comparisons, strain SM30(T) was most closely related to Pleomorphomonas oryzae DSM 16300(T), with a low similarity of 94.17 %. One of the lanthanide metals, lanthanum, could enhance its growth slightly on methanol. Phylogenetic trees, based on the mxaF, xoxF and cpn60 genes of SM30(T) showed its distinct phylogenetic position with respect to species with validly published names. Polymerase chain reaction (PCR) amplification of the nifH and growth on nitrogen-free medium indicated that strain SM30(T) is a diazotroph. The major cellular fatty acids were summed feature 8 (containing 18:1 omega 7c and 18:1 omega 6c) and cyclo 19:0 omega 8c. The major quinone was ubiquinone 10. The DNA G+C content was 74.6 mol%. Based on the genotypic and phenotypic characteristics, strain SM30(T) represents a novel genus and species, for which the name Oharaeibacter diazotrophicus gen. nov., sp. nov. is proposed with the type strain SM30(T) (= NBRC 111955(T) = DSM 102969(T)). KAKENHIMinistry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of ScienceGrants-in-Aid for Scientific Research (KAKENHI) [15H04476]; Advanced Low Carbon Technology Research and Development Program (ALCA), JST; China Scholarship CouncilChina Scholarship Council; Grants-in-Aid for Scientific ResearchMinistry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of ScienceGrants-in-Aid for Scientific Research (KAKENHI) [15H04476] Funding Source: KAKEN This work was partially supported by KAKENHI (15H04476) to AT, Advanced Low Carbon Technology Research and Development Program (ALCA), JST to AT, and financial support from the China Scholarship Council to HL.

Sitagliptin, the first of a new class of dipeptidyl peptidase-4 (DPP-4)-inhibitory oral antihyperglycaemic drugs (OHDs), was introduced in Japan in December 2009. In April 2010 a safety alert was issued regarding the risk of serious hypoglycaemic events, and prescribers were recommended to reduce the dose of sulfonylurea (i.e. glimepiride, glibenclamide [glyburide] or gliclazide) in patients receiving a combination of sulfonylurea and sitagliptin. A propensity score-matched cohort study was performed using Japanese pharmacy prescription receipt data for OHDs in order to confirm reported changes in OHD prescription behaviour for patients receiving sitagliptin before and after the safety alert. Prescription data from about 6,500 medical institutions throughout Japan during December 2009 to 31 December 2010 were randomly collected from 300 pharmacies, covering 82,064 patients with 629,955 prescriptions for OHDs. Patients who had received a sulfonylurea and sitagliptin (1,788 patients/3,576 prescriptions) before the safety alert were designated as the DPP-4 group. Patients who had received a sulfonylurea but not sitagliptin (30,963 patients/61,926 prescriptions) before the alert were designated as the non-DPP-4 group. Propensity score matching was employed to match baseline characteristics, such as age, sex, type of OHD, metformin use, type of prescribers period for measuring baseline period and type of prescribers’ institutions, for 1,783 patients from each group. In the matched cohort, logistic regression analysis was conducted to compare prescription trends before and after the alert. The primary outcome measure of this study was dose of glimepiride, glibenclamide or gliclazide prescribed for DPP-4 and non-DPP-4 patients. In the propensity score-matched cohort, the proportion of glimepiride dose >2 mg of DPP-4 patients was reduced from 45.8 % in Period 1 (before the alert) to 37.5 % in Period 2 (after the alert) (odds ratio [OR] 0.71; 95 % CI 0.579–0.870), whereas in the case of non-DPP-4 patients the proportion was changed from 28.9 % to 29.5 % in the matched cohort (OR 1.03; 95 % CI 0.868–1.215). The mean prescribed glimepiride dose in DPP-4 patients was also reduced from 2.79 ± 1.81 mg in Period 1 (before the alert) to 2.38 ± 1.71 mg in Period 2 (after the alert) [p

Summary What is known and Objective: The increasing cost of drug research and development and the decreasing number of new drugs being launched are serious issues for pharmaceutical companies. Biomarkers for predicting drug effectiveness are regarded as useful tools for combating these trends. However, the extent to which these biomarkers actually help in improving drug development is unclear. Here, we investigated the efficiency of biomarker usage in oncology drug development by focusing on stratification markers. Methods: Anti-tumour agents for which clinical studies were initiated between 1998 and 2009 were identified using commercially available data sources, and clinical trials registered in ClinicalTrials.gov were examined to identify the use of stratification marker. Phase transition probability for each clinical phase was calculated and analysed along with various other factors that may affect the efficiency of the development process. Results and Discussion: Of 908 anti-tumour agents identified, 121 (13·3%) utilized stratification markers in their clinical studies. Phase I, II and III transition probabilities for all agents were 76·4%, 50·8% and 58·5%, respectively. Corresponding Phase I, II and III transition probabilities of agents developed with stratification markers of 90·4%, 69·0% and 85·0%, respectively, were significantly higher than those for agents without stratification markers. Orphan designation positively affected phase transition probabilities of agents without stratification markers in all phases, while it did not affect transition probabilities of agents with stratification markers, except for Phase II. This shows that stratification markers help improve the probability of success in the development of agents without orphan designation. What is new and Conclusion: Stratification markers contribute to improving the efficiency of development of anti-cancer drugs. The majority of non-orphan drugs are still being developed without stratification markers. Finding reliable stratification markers for all drugs should improve the success rates in drug development.

Objective There is little evidence concerning risk factors for sudden cardiac death (SCD) among Asians. Patients and methods A prospective, nested, case-control study of Japanese patients aged between 30 and 84 years was undertaken using data collected from 26 870 participants in cardiovascular risk surveys conducted in four communities between 1975 and 2005. The incidence of SCD was ascertained by systematic surveillance, with 239 cases of SCD identified over this period. For each case of SCD, three control patients were selected, matched by age, sex, examination year, follow-up time, and community. Results Hypertension, diabetes mellitus, smoking, major ST-T abnormalities, left high amplitude R waves, and increased heart rate (≥77 beat/min) were all independently associated with a 1.5-3.2-fold increase in SCD risk, whereas no associations were observed for body mass index and hypercholesterolemia. The population-attributable fraction [95% confidence interval (CI)] was 23.0% (2.9-39.0) for hypertension, 15.3% (3.8-25.5) for current smoking, 14.5% (8.0-20.5) for major ST-T abnormalities, and 8.1% (2.2-13.7) for diabetes mellitus. The number of SCD risk factors (hypertension, diabetes, smoking, and ECG abnormalities) was positively associated with increased SCD risk. The odds ratio for increased SCD risk with three or more risk factors versus zero risk factors was 5.76 (95% CI 3.20-10.39). Conclusions Among the Japanese population, hypertension, smoking, major ST-T abnormalities, left high amplitude R waves, and diabetes mellitus were associated with an increased incidence of SCD, whereas there were no associations of body mass index or hypercholesterolemia with SCD incidence.

Japanese government has started to implement several actions to promote the use of generics; however, the generic penetration rate in value advanced rather slowly from 15.4% in March 2006 to 18.7% in December 2009. Japanese pharmaceutical market has at least two unique facts which differentiate from other markets: timing of generics launch and pricing. These unique features may require a new entrant to consider the different marketing strategy. In this article, we observed that the penetration rate varies among therapeutic categories and the penetration curve for vasodilators, miscellaneous antineoplastics, and synthetic antibacterials is similar. Particularly, these categories had a launch of major original drugs within the examined period and the logistic regression for each category indicated that the reflection point of the curve was 21, 33, and 39 days after the generics launch, accordingly. As previous research suggests that the estimated sales revenue of the original drug is considered as a key determinant for generic drug penetration even in Japan. Japanese generics market will likely grow with a support of government generic promotion policy and the upcoming patent expiry of blockbusters. It is important to consider the entry strategy by therapeutic category and plan the early market penetration strategy.

Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.

製薬業界は，大型製品の特許満了，研究開発の遅れ，新規上市品目数の減少，後発医薬品の市場浸透，薬価制度の変更と，近年，急速に事業環境が大きく変化しており，新たなビジネスモデルの確立が必要となってきている。これらの問題に対しての打開策として，海外大手製薬企業は，他社との経営統合，新興諸国市場への進出，後発医薬品事業の展開など，新しいビジネスモデルの構築を行っており，一方，自社開発製品の海外展開により成長してきた国内大手製薬企業は，海外企業の買収等を行うことで，打開策を模索している。国内では，海外に比べ遅れていた後発医薬品の使用促進が国の主導のもと行われており，国内事業に特化している新薬開発型製薬企業にとっては，製品の特許満了後の後発医薬品へのシフトによる減収リスクが大きくなってきており，収益を長期収載品に依存するビジネスモデルの変革を余儀なくされている。このように，事業環境の変化に対応すべく，近年，製薬企業が取っている動きの大きなポイントとなるものは，1）医薬品兼業企業による経営統合，2）新興諸国への取組み強化，3）後発医薬品の取組み強化，4）企業買収による海外展開に分けられる。今後のジネスモデルの確立と成功が待たれる。

Thiosulfate-oxidizing sox gene homologues were found at four loci (I, II, III, and IV) on the genome of Bradyrhizobium japonicum USDA110, a symbiotic nitrogen-fixing bacterium in soil. In fact, B. japonicum USDA110 can oxidize thiosulfate and grow under a chemolithotrophic condition. The deletion mutation of the soxY 1 gene at the sox locus I, homologous to the sulfur-oxidizing (Sox) system in Alphaproteobacteria , left B. japonicum unable to oxidize thiosulfate and grow under chemolithotrophic conditions, whereas the deletion mutation of the soxY 2 gene at sox locus II, homologous to the Sox system in green sulfur bacteria, produced phenotypes similar to those of wild-type USDA110. Thiosulfate-dependent O 2 respiration was observed only in USDA110 and the soxY 2 mutant and not in the soxY 1 mutant. In the cells, 1 mol of thiosulfate was stoichiometrically converted to approximately 2 mol of sulfate and consumed approximately 2 mol of O 2 . B. japonicum USDA110 showed 14 CO 2 fixation under chemolithotrophic growth conditions. The CO 2 fixation of resting cells was significantly dependent on thiosulfate addition. These results show that USDA110 is able to grow chemolithoautotrophically using thiosulfate as an electron donor, oxygen as an electron acceptor, and carbon dioxide as a carbon source, which likely depends on sox locus I including the soxY 1 gene on USDA110 genome. Thiosulfate oxidation capability is frequently found in members of the Bradyrhizobiaceae , which phylogenetic analysis showed to be associated with the presence of sox locus I homologues, including the soxY 1 gene of B. japonicum USDA110.

Bradyrhizobium japonicum is a facultative chemolithoautotroph capable of using thiosulfate and H(2) as an electron donor and CO(2) as a carbon source. In B. japonicum USDA110, the mutant of cbbL gene encoding a large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) was unable to grow using thiosulfate and H(2) as an electron donor. The cbbL deletion mutant was able to grow and oxidize thiosulfate in the presence of succinate. These results showed that the major route of CO(2) fixation for thiosulfate-dependent chemoautotrophic growth is the Calvin-Benson-Bassham cycle involving RuBisCO in B. japonicum.

This paper reviews the institutional factors in Japan that affect the market exclusivity period for new drugs. The factors which directly affect the period are (1) statutory subject matter of patent protection, (2) patent term extension, and (3) restriction of the entry of generic drugs (market exclusivity right or data protection system). Other factors include (4) the experimental use exception (the so-called Bolar provision) and (5) compulsory license. In addition, the impacts of these factors on both brand-named manufacturers and generic drug manufacturers under the specific circumstances of the Japanese pharmaceutical market, such as the influence of the healthcare insurance system or the drug price control system, are discussed.

An 8-year-old boy presented with acute osteomyelitis in his right patella. Radiographs demonstrated an osteolytic lesion in the superior pole. Curettage was performed, followed by the administration of antibiotics. Four months later, the patient’s symptoms completely disappeared. Our case suggests that acute osteomyelitis of the patella is caused by hematogenous spread from surface, paralleling unique intraosseous arterial patterns.

Summary What is known and objective Decline in research and development (R&D) productivity and changes in the business environment have led to pharmaceutical company management to strive to improve R&D productivity. This decline is widely considered to be a major cause of industry consolidation and has received increased scholarly attention. This study aims to construct an R&D productivity map to visualize the industry's R&D productivity and to identify similarity in corporate actions with a view to investigate whether there is a relationship between deterioration in R&D productivity and industry consolidation. Methods Research and development productivity is decomposed into two subprocesses to measure productivity: R&D efficiency and R&D effectiveness, and scores were calculated using a two-stage data envelopment analysis (DEA). The map is then constructed by projecting outputs. To identify any relationship between DEA scores and merger and acquisition transactions, a multiple regression model is employed. Results and discussion Data on 21 global pharmaceutical companies, statistical results indicated that companies with lower R&D efficiency scores were more likely to engage in consolidation. Three US companies that were least successful in terms of R&D effectiveness, as measured by our indicators, were either acquired or changed their business model. Conclusion The R&D productivity map is a useful means for visualizing productivity among companies. By grouping companies into four groups, behavioural commonalities can be observed. The R&D productivity map should be useful for monitor the industry's productivity and help to improve it.

Streptococcus intermedius secretes a human-specific cytolysin, intermedilysin (ILY), which is considered to be the major virulence factor of this pathogen. We screened for a repressor of ily expression by using random gene disruption in a low-ILY-producing strain (PC574). Three independent high-ILY-producing colonies that had plasmid insertions within a gene that has high homology to lacR were isolated. Validation of these observations was achieved through disruption of lacR in strain PC574 with an erythromycin cassette, which also led to higher hemolytic activity, increased transcription of ily , and higher cytotoxicity against HepG2 cells, compared to the parental strain. The direct binding of LacR within the ily promoter region was shown by a biotinylated DNA probe pulldown assay, and the amount of ILY secreted into the culture supernatant by PC574 cells was increased by adding lactose or galactose to the medium as a carbon source. Furthermore, we examined lacR nucleotide sequences and the hemolytic activity of 50 strains isolated from clinical infections and 7 strains isolated from dental plaque. Of the 50 strains isolated from infections, 13 showed high ILY production, 11 of these 13 strains had one or more point mutations and/or an insertion mutation in LacR, and almost all mutations were associated with a marked decline in LacR function. These results strongly suggest that mutation in lacR is required for the overproduction of ILY, which is associated with an increase in pathogenicity of S. intermedius .

In light of the Japan Patent Office's revised examination guidelines, what are the potential problems of protecting advanced biomedical methods related to medical activity?

Background Sitagliptin, the first of a new class of dipeptidyl peptidase-4 (DPP-4)-inhibitory oral antihyperglycemic drugs (OHDs), was introduced in Japan in December 2009. In April 2010 a safety alert was issued regarding the risk of serious hypoglycemic events when the drug is used in combination with high-dose sulfonylureas (SUs). Objective To investigate trends in prescription of OHDs before and after the launch of sitagliptin, and before and after the safety alert, in order to evaluate changes in the prescribing behavior of various groups of physicians in response to the safety alert. Setting Japan. Method Prescription data from 6,500 institutions, randomly collected from 300 Japanese pharmacies were used. A cohort of 87,678 patients with 813,374 prescriptions for OHDs, among which 464,079 included SUs (glimepiride: 317,423), was collected from August 2009 to 31 December 2010. Logistic regression analysis was conducted. Main Outcome Measure Prescription trends for sitagliptin and SUs, stratified by age, gender, types of prescribers and institutions. Results The safety alert recommending a reduction of SU dosing was well reflected in prescriptions issued after the alert (glimepiride dose reduction from 2.78 ± 1.86 mg to 2.32 ± 1.68), especially in prescriptions issued by diabetes specialists (from 2.27 ± 1.81 mg to 1.87 ± 1.47 mg). The dose of background SUs in patients who started sitagliptin early was higher (before alert: 2.70 ± 1.80 mg, after alert: 2.51 ± 1.74 mg) than in patients without experience of sitagliptin (2.12 ± 1.57 mg). This may indicate that patients receiving high-dose SUs were selected for sitagliptin, and this might be a factor in the high frequency of hypoglycemia in the early launch phase of sitagliptin. Conclusion The sitagliptin safety alert had a clear impact on prescribing behavior, but the impact appeared to depend on prescribers’ backgrounds. Our findings should be helpful for developing a safer drug launching strategy for new classes of drugs in established categories.