HexR Transcription Factor Contributes to Pseudomonas cannabina pv. alisalensis Virulence by Coordinating Type Three Secretion System Genes

Pseudomonas cannabina pv. alisalensis (Pcal) causes bacterial blight on cabbage. We previously conducted a screening for reduced virulence using Tn5 transposon mutants and identified one of the transcriptional factors, HexR, as a potential Pcal virulence factor. However, the role of HexR in plant pathogenic Pseudomonas virulence has not been investigated well. Here, we demonstrated that the Pcal hexR mutant showed reduced disease symptoms and bacterial populations on cabbage, indicating that HexR contributes to Pcal virulence. We used RNA-seq analysis to characterize the genes regulated by HexR. We found that several type three secretion system (T3SS)-related genes had lower expression of the Pcal hexR mutant. Five genes were related to T3SS machinery, two genes were related to type three helper proteins, and three genes encoded type three effectors (T3Es). We also confirmed that T3SS-related genes, including hrpL, avrPto, hopM1, and avrE1, were also down-regulated in the Pcal hexR mutant both in culture and in vivo by using RT-qPCR. T3SS functions to suppress plant defense in host plants and induce hypersensitive response (HR) cell death in non-host plants. Therefore, we investigated the expression profiles of cabbage defense-related genes, including PR1 and PR5, and found that the expressions of these genes were greater in the Pcal hexR mutant. We also demonstrated that the hexR mutant did not induce HR cell death in non-host plants, indicating that HexR contributes in causing HR in nonhost plants. Together, these results indicate that the mutation in hexR leads to a reduction in the T3SS-related gene expression and thus an impairment in plant defense suppression, reducing Pcal virulence.

Exertional Desaturation Is More Severe in Idiopathic Pulmonary Fibrosis Than in Other Interstitial Lung Diseases

OBJECTIVE

Interstitial lung disease (ILD) is classified into several disease groups. Among them, idiopathic pulmonary fibrosis (IPF) has higher incidence and poor prognosis; therefore, it is important to characterize specific IPF symptoms. Exercise desaturation is a strong factor related to mortality in patients with ILD. Thus, the purpose of this study was to compare the degree of oxygen desaturation between IPF and other ILD (non-IPF ILD) patients during exercise, using the 6-minute walk test (6MWT).

METHODS

This retrospective study included 126 stable patients with ILD who underwent 6MWT in our outpatient department. The 6MWT was used to assess desaturation during exercise, 6-minute walk distance (6MWD), and dyspnea at the end of exercise. In addition, patient characteristics and pulmonary function test results were recorded.

RESULTS

Study subjects were divided into 51 IPF patients and 75 non-IPF ILD patients. The IPF group had significantly lower nadir oxygen saturation determined by pulse oximetry (SpO2) during 6MWT than the non-IPF ILD group (IPF, 86.5 ± 4.6%; non-IPF ILD, 88.7 ± 5.3%; p = 0.02). The significant association between the nadir SpO2 and IPF or non-IPF ILD grouping remained even after adjusting for gender, age, body mass index, lung function, 6MWD, and dyspnea (β = -1.62; p <0.05).

CONCLUSION

Even after adjusting for confounding factors, IPF patients had lower nadir SpO2 during 6MWT. Early assessment of exercise desaturation using the 6MWT may be more important in patients with IPF compared with patients with other ILDs.

Impact of postoperative physical activity on the development of pneumonia in the subacute phase after esophagectomy in patients with esophageal cancer: A retrospective cohort study

PURPOSE

Physical activity is important to improve recovery following surgery. This study investigated the impact of physical activity on the development of pneumonia after radical esophagectomy in patients with thoracic esophageal cancer in the subacute phase from postoperative day 11 to hospital discharge.

METHODS

This retrospective cohort study included 83 patients who underwent radical esophagectomy for esophageal cancer between 2016 and 2022. Physical activity was measured using an activity tracker, and the average number of steps between postoperative days 8 and 10 was examined. The primary outcome was pneumonia (Clavien-Dindo classification 2 or higher) developing between postoperative day 11 and hospital discharge. We used the receiver operating characteristic (ROC) curve analysis to calculate the optimal cutoff value of physical activity that can predict the development of pneumonia and define low physical activity. We used logistic regression analysis to investigate the impact of low physical activity on postoperative pneumonia.

RESULTS

Pneumonia developed in 10 patients (12.0%) during the observation period. The optimal cutoff value of physical activity for predicting pneumonia was 1494 steps per day (sensitivity: 60.0%, specificity: 89.0%, area under the curve: 0.743). In multivariate analysis, low physical activity was an independent predictor of incident pneumonia [odds ratio: 12.10, 95% confidence interval: 2.21-65.90, p = 0.004], with adjustment for age, gastric tube reconstruction route, and postoperative recurrent nerve palsy.

CONCLUSIONS

Physical activity following radical esophagectomy in patients with thoracic esophageal cancer was an independent predictor of the development of pneumonia in the subacute phase after radical esophagectomy.

Pseudomonas aegrilactucae sp. nov. and Pseudomonas morbosilactucae sp. nov., pathogens causing bacterial rot of lettuce in Japan

Phytopathogenic bacterial strains (MAFF 301350T, MAFF 302030T and MAFF 302046), isolated from lettuce (Lactuca sativa var. capitata) with bacterial rot disease in Japan, were subjected to polyphasic characterization to determine their taxonomic affiliations. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with polar flagella and rod-shaped. The results of similarity searches and phylogenetic analyses based on the 16S rRNA gene sequences, as well as the analysis results of the cellular fatty acid composition and genomic DNA G+C content indicated that these strains belong to the genus Pseudomonas . Phylogenetic analyses using the rpoD gene sequences and phylogenomic analyses of the whole genome sequences grouped them into the Pseudomonas putida group (MAFF 301350T) and the Pseudomonas fluorescens group (MAFF 302030T and MAFF 302046), but the phylogenetic positions of the strains did not match those of any known Pseudomonas species. The average nucleotide identity and digital DNA–DNA hybridization values between the strains and their closely related species were lower than the thresholds for prokaryotic species delineation (95–96 and 70 %, respectively). Phenotypic characteristics, pathogenicity toward lettuce, cellular fatty acid composition and whole-cell MALDI-TOF mass spectrometry profiles could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that the strains represent two novel species of the genus Pseudomonas , Pseudomonas aegrilactucae sp. nov. for MAFF 301350T and Pseudomonas morbosilactucae sp. nov. for MAFF 302030T and MAFF 302046. The respective type strains are MAFF 301350T (= ICMP 23989T) and MAFF 302030T (= ICMP 24377T).

Pseudomonas petroselini sp. nov., a pathogen causing bacterial rot of parsley in Japan

Phytopathogenic bacterial strains (MAFF 311094T, MAFF 311095, MAFF 311096 and MAFF 311097), which were isolated from rot lesions of parsley (Petroselinum crispum) sampled in Miyagi, Japan, were subjected to polyphasic characterization to determine their taxonomic position. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella and rod-shaped. The 16S rRNA gene sequences analyses revealed that the strains belong to the genus Pseudomonas , exhibiting the highest sequence similarity to Pseudomonas sivasensis P7T (99.93% sequence similarity), Pseudomonas cyclaminis MAFF 301449T (99.93 %), Pseudomonas extremaustralis 14-3T (99.86 %), Pseudomonas kitaguniensis MAFF 212408T (99.86 %) and Pseudomonas antarctica CMS 35T (99.79 %). The genomic DNA G+C content was 60.1 mol%, and the major cellular fatty acids (>5 % of the total fatty acids) were C16:0, summed feature 3 (C16:1 ω7c/C16:1 ω6c), summed feature 8 (C18:1 ω7c/C18:1 ω6c) and C17:0 cyclo. The rpoD sequence-based phylogenetic and whole genome-based phylogenomic analyses demonstrated that the strains are a member of the Pseudomonas fluorescens subgroup, but their phylogenetic position does not match those of any members of this subgroup. The average nucleotide identity and digital DNA–DNA hybridization values between the strains and their closely related species were ≤90.64% and ≤41.9 %, respectively, which were below the thresholds for prokaryotic species delineation (95–96 and 70%, respectively). Phenotypic characteristics, pathogenicity toward parsley and cellular fatty acid composition could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data presented in this study revealed that the strains constitute a novel Pseudomonas species, for which we propose the name Pseudomonas petroselini sp. nov., with MAFF 311094T (=ICMP 24279T) being the type strain.

The effect of home-based preoperative pulmonary rehabilitation before lung resection: A retrospective cohort study

OBJECTIVES

This study aimed to assess the effect of home-based preoperative pulmonary rehabilitation (HBPPR) on the incidence of postoperative complications, length of stay (LOS), and duration of intercostal catheterization in non-small cell lung cancer (NSCLC) patients who underwent lung resection.

MATERIALS AND METHODS

In this retrospective cohort study, 144 patients who underwent lung resection were recruited, 51 of whom received HBPPR, comprising respiratory muscle training and was supervised (for patients undergoing it for the first time). Patients continued these programs for 2-4 weeks during the preoperative waiting period, in their homes. Data on postoperative complications graded according to the Clavien-Dindo classification, LOS, and intercostal catheterization duration were collected from medical records. These outcomes were compared between the HBPPR and non-HBPPR groups using Fisher's exact test and Wilcoxon rank sum test, after 1:1 propensity score matching to avoid selection bias.

RESULTS

Forty-nine matched pairs were extracted using propensity score matching. HBPPR reduced the onset of postoperative complications (p = 0.04), with the relative ratio (RR) for Clavien-Dindo Class I postoperative complications showing a significant difference (RR 0.55, 95% CI 0.30-1.02; p = 0.05), whereas RRs for the other Clavien-Dindo classes were not statistically significant. There was no significant difference in LOS or the duration of intercostal catheterization.

CONCLUSION

HBPPR reduced the incidence of Clavien-Dindo Class I postoperative complications after lung resection. Implementing HBPPR practices in a clinical setting would benefit patients unable to receive supervised preoperative pulmonary rehabilitation due to access barriers, time, and financial constraints.

Unexpected genomic features of high current density-producing Geobacter sulfurreducens strain YM18

Geobacter sulfurreducens produces high current densities and it has been used as a model organism for extracellular electron transfer studies. Nine G. sulfurreducens strains were isolated from biofilms formed on an anode poised at -0.2 V (vs SHE) in a bioelectrochemical system in which river sediment was used as an inoculum. The maximum current density of an isolate, strain YM18 (9.29 A/m2), was higher than that of the strain PCA (5.72 A/m2), the type strain of G. sulfurreducens, and comparable to strain KN400 (8.38 A/m2), which is another high current-producing strain of G. sulfurreducens. Genomic comparison of strains PCA, KN400 and YM18 revealed that omcB, xapD, spc and ompJ, which are known to be important genes for iron reduction and current production in PCA, were not present in YM18. In the PCA and KN400 genomes, two and one region(s) encoding CRISPR/Cas systems were identified, respectively, but they were missing in the YM18 genome. These results indicate that there is genetic variation in the key components involved in extracellular electron transfer among G. sulfurreducens strains.

Pseudomonas lactucae sp. nov., a pathogen causing bacterial rot of lettuce in Japan

Two phytopathogenic bacteria, MAFF 301380T and MAFF 301381, isolated from rot lesions of lettuce (Lactuca sativa L. var. capitata L.) in Japan, were characterized using a polyphasic approach. The cells were Gram-reaction-negative, aerobic, non-spore-forming, rod-shaped and motile with one to three polar flagella. Analysis of the 16S rRNA gene sequences showed that the strains belong to the genus Pseudomonas and are closely related to Pseudomonas cedrina subsp. cedrina CFML 96-198T (99.72 %), Pseudomonas cedrina subsp. fulgida P515/12T (99.65 %), Pseudomonas gessardii DSM 17152T (99.51 %), Pseudomonas synxantha DSM 18928T (99.44 %), Pseudomonas libanensis CIP 105460T (99.44 %) and Pseudomonas lactis DSM 29167T (99.44 %). The genomic DNA G+C content was 60.4 mol% and the major fatty acids consisted of summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), C16 : 0 and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c). Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup but formed a monophyletic and robust clade separated from their closest relatives. The average nucleotide identity and digital DNA-DNA hybridization values between the strains and their closely related species were 88.65 % or less and 36.3 % or less, respectively. The strains could be distinguished from their closest relatives by phenotypic characteristics, pathogenicity towards lettuce and whole-cell MALDI-TOF MS profiles. The evidence presented in this study supports the classification of the strains as representing a novel Pseudomonas species, for which we propose the name Pseudomonas lactucae sp. nov., with the type strain MAFF 301380T (=ICMP 23838T).

Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114

Mitsuaria sp. TWR114 is a biocontrol agent against tomato bacterial wilt (TBW). We aimed to gain genomic insights relevant to the biocontrol mechanisms and colonization ability of this strain. The draft genome size was found to be 5,632,523 bp, with a GC content of 69.5%, assembled into 1144 scaffolds. Genome annotation predicted a total of 4675 protein coding sequences (CDSs), 914 pseudogenes, 49 transfer RNAs, 3 noncoding RNAs, and 2 ribosomal RNAs. Genome analysis identified multiple CDSs associated with various pathways for the metabolism and transport of amino acids and carbohydrates, motility and chemotactic capacities, protection against stresses (oxidative, antibiotic, and phage), production of secondary metabolites, peptidases, quorum-quenching enzymes, and indole-3-acetic acid, as well as protein secretion systems and their related appendages. The genome resource will extend our understanding of the genomic features related to TWR114's biocontrol and colonization abilities and facilitate its development as a new biopesticide against TBW.

Pseudomonas cyclaminis sp. nov., a pathogen causing bacterial bud blight of cyclamen in Japan

Five phytopathogenic bacterial strains, MAFF 301449^T, MAFF 301450, MAFF 301451, MAFF 301452, and MAFF 301453, which were isolated from bud blight lesions of cyclamen (Cyclamen persicum Mill.) in Miyagi, Japan, were subjected to polyphasic taxonomic characterisation. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one to five polar flagella, and rod-shaped. Analysis of 16S rRNA gene sequences showed that they belong to the genus Pseudomonas, with Pseudomonas extremaustralis 14-3^T (99.79 % sequence similarity), Pseudomonas trivialis DSM 14937^T (99.79 %), Pseudomonas poae DSM 14936^T (99.72 %), and Pseudomonas antarctica CMS 35^T (99.72 %) as their relatives. The genomic DNA G+C content was 60.3 mol% and the major fatty acids (>5 % of the total fatty acids) were C_16 : 0, summed feature 3 (C_16 : 1 ω7c/C_16 : 1 ω6c), summed feature 8 (C_18 : 1 ω7c/C_18 : 1 ω6c), and C_17 : 0 cyclo. Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup, but form a monophyletic and robust clade separated from their relatives. Average nucleotide identity and digital DNA-DNA hybridisation analyses with the closely related Pseudomonas species corroborated their novel species status. The strains were differentiated from their relatives by phenotypic characteristics, pathogenicity towards cyclamen, cellular fatty acid composition, and whole-cell MALDI-TOF mass spectrometry profiles. Based on the phenotypic, chemotaxonomic, and genotypic data obtained, we conclude that the strains represent a novel Pseudomonas species, for which we propose the name Pseudomonas cyclaminis sp. nov.; the type strain is MAFF 301449^T (=ICMP 23720^T).

Detection and identification of Xanthomonas campestris pv. campestris and pv. raphani by multiplex polymerase chain reaction using specific primers

Black rot and bacterial spots threaten the cultivation of cruciferous vegetables worldwide, and the development of a method that can easily detect, identify, and distinguish their respective pathogens Xanthomonas campestris pv. campestris (Xcc) and X. campestris pv. raphani (Xcr) is required. Multiple whole-genome sequences of Xcc and Xcr were aligned to identify specific regions and subsequently design gene markers. A region present in Xcr, but absent in Xcc, was detected, which was approximately 11.5 kbp in length, sandwiched between the serine protease homolog (SPH) and nicotinate phosphoribosyltransferase gene (pncB). It contained putative cellulose synthesis-related genes, whereas Xcc only had a modified cellulose synthase gene. Designed primers were pncB_fw1 and pncB_fw2 (from the pncB gene), Xcc_rv1 and Xcc_rv2 (from the modified cellulose synthesis gene), and Xcr_rv1 and Xcr_rv2 (from the putative first and second open reading frames of the gene cluster). PCR using pncB_fw1 and Xcc_rv1, or pncB_fw2 and Xcc_rv2, amplified DNA fragments only in Xcc and X. campestris pv. incanae (Xci). Xci is the causal agent of black rot of garden stock and closely related to Xcc. PCR using pncB_fw1 and Xcr_rv1, or pncB_2 and Xcr_rv2, amplified DNA fragments only in Xcr. Multiplex PCR analysis easily distinguished Xcc and Xcr from bacterial colonies isolated on growth media and detected the pathogen in symptomatic leaves. Multiplex nested PCR detected the contamination of one seed with Xcc and/or Xcr infection from 1000 seeds. Therefore, the PCR primers designed in this study therefore helped detect and discriminate between Xcc and Xcr. KEY POINTS: • Xanthomonas campestris pv. campestris (Xcc) and pv. raphani (Xcr) were investigated. • Novel primers were designed following whole-genome comparison analyses. • Multiplex PCR with new primers distinguished Xcc and Xcr simultaneously.

Pseudomonas allii sp. nov., a pathogen causing soft rot of onion in Japan

Six phytopathogenic bacterial strains, MAFF 301512, MAFF 301513, MAFF 301514^T, MAFF 301515, MAFF 301516 and MAFF 301517, were isolated from soft rot lesions of onion (Allium cepa L.) in Japan. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella and rod-shaped. Analysis of their 16S rRNA gene sequences showed that they belong to the genus Pseudomonas, with the highest similarities to Pseudomonas poae DSM 14936^T (99.86 %), Pseudomonas simiae OLi^T (99.85 %), Pseudomonas trivialis DSM 14937^T (99.79 %) and Pseudomonas extremorientalis KMM 3447^T (99.79 %). Their genomic DNA G+C content was 60.9 mol% and the major fatty acids (>5 % of the total fatty acids) present were C_16 : 0, summed feature 3 (C_16 : 1 ω7c/C_16 : 1 ω6c), summed feature 8 (C_18 : 1 ω7c /C_18 : 1 ω6c) and C_17 : 0 cyclo. Phylogenetic and phylogenomic analyses based on the rpoD gene and whole genome sequences, respectively, demonstrated that the strains belong to the Pseudomonas fluorescens subgroup, but form a monophyletic and robust clade, with Pseudomonas azotoformans as their neighbour. Between the strains and P. azotoformans, the average nucleotide identity scores were 95.63-95.70 %, whereas the digital DNA-DNA hybridization scores of the strains against their closest relatives, including P. azotoformans, were 65.4 % or less, which are lower than the 70 % cut-off for prokaryotic species delineation. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity in onion and cellular fatty acid composition. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel Pseudomonas species, proposed to be named Pseudomonas allii sp. nov., with MAFF 301514^T (=ICMP 23680^T) being the type strain.

Pseudomonas brassicae sp. nov., a pathogen causing head rot of broccoli in Japan

Phytopathogenic bacteria, MAFF 212426, MAFF 212427T, MAFF 212428 and MAFF 212429, were isolated from head rot lesions of broccoli (Brassica oleracea L. var. italica Plenck) in Hokkaido, Japan, and subjected to polyphasic taxonomic characterization. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella, rod-shaped and formed pale yellow colonies. Results of 16S rRNA gene sequence analysis showed that they belong to the genus Pseudomonas with the highest similarity to ‘Pseudomonas qingdaonensis’ JJ3T (99.86 %), Pseudomonas laurentiana GSL-010T (99.22 %), Pseudomonas huaxiensis WCHPs060044T (99.01 %), Pseudomonas japonica NBRC 103040T (98.87 %) and Pseudomonas alkylphenolica KL28T (98.73 %). The genomic DNA G+C content was 63.4 mol% and the major fatty acids (>5 % of the total fatty acids) were summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c / C18 : 1 ω6c) and C17 : 0 cyclo. Multilocus sequence analysis using the partial rpoD, gyrB and rpoB gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas putida group, but form a monophyletic, robust clade separated from their closest relatives. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values corroborated their novel species status, with 88.39 % (ANI) and 35.8 % (dDDH) as the highest scores with ‘P. qingdaonensis’ JJ3T. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity on broccoli, and whole-cell MALDI-TOF mass spectrometry profiles. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel Pseudomonas species, for which the name Pseudomonas brassicae sp. nov. is proposed. The type strain is MAFF 212427T (=ICMP 23635T).

Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions

The kiwifruit bacterial canker (Pseudomonas syringae pv. actinidiae; Psa) causes severe damage to kiwifruit production worldwide. Psa biovar 6 (Psa6), which was isolated in Japan in 2015, produces two types of phytotoxins: coronatine and phaseolotoxin. To elucidate the unique virulence of Psa6, we performed transcriptomic analysis of phytotoxin synthesis genes and type III effector genes in in vitro cultivation using various media. The genes related to phytotoxin synthesis and effectors of Psa6 were strictly regulated in the coronatine-inducing mediums (HS and HSC); 14 of 23 effector genes and a hrpL sigma factor gene were induced at 3 h after transferring to the media (early-inducible genes), and phytotoxin synthesis genes such as argD of phaseolotoxin and cfl of coronatine were induced at 6 and 12 h after transferring to the media (late-inducible genes). In contrast, induction of these genes was not observed in the hrp-inducing medium. Next, to examine whether the changes in gene expression in different media is specific to Psa6, we investigated gene expression in other related bacteria. For Psa biovar 1 (Psa1), biovar 3 (Psa3), and P. s. pv. glycinea (Psg), no clear trends were observed in expression behavior across various culture media and incubation times. Therefore, Psa6 seems to exert its virulence efficiently by using two phytotoxins and effectors according to environmental changes. This is not seen in other biovars and pathovars, so it is thought that Psa6 has acquired its own balance of virulence.

Pseudomonas kitaguniensis sp. nov., a pathogen causing bacterial rot of Welsh onion in Japan

Five Gram-reaction-negative, aerobic, motile with one to three polar flagella, rod-shaped bacterial strains, MAFF 212408T, MAFF 212409, MAFF 212410, MAFF 301498 and MAFF 730085, were isolated from diseased Welsh onion (Allium fistulosum L.) in Japan. Analysis of their 16S rRNA gene sequences showed that they belong to the genus Pseudomonas with the highest similarity to Pseudomonas extremaustralis 14-3T (99.86 %), Pseudomonas antarctica CMS 35T (99.79 %) and Pseudomonas poae DSM 14936T (99.72%). The genomic DNA G+C content was 59.5 mol% and the major fatty acids (>5 %) were summed feature 3, C16 : 0, summed feature 8 and C12 : 0 2-OH. Multilocus sequence analysis using the rpoD, gyrB and rpoB gene sequences and phylogenomic analysis based on the 90 core genes demonstrated that the strains are members of the P. fluorescens subgroup, but are distant from all closely related species. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analysis confirmed low genomic relatedness to their closest relatives [below the recommended thresholds of 95 % (ANI) and 70 % (dDDH) for prokaryotic species delineation]. The strains were characterized by using API 20NE and Biolog GEN III tests, and inoculation tests in Welsh onion, showing that they are phenotypically differentiated from their closest relatives. Based on the genetic and phenotypic evidence, the strains should be classified as representing a novel species, for which the name Pseudomonas kitaguniensis sp. nov. is proposed. The type strain is MAFF 212408T (=ICMP 23530T).

113 Effect of antioxidants on motility and fertility of liquid-stored bovine sperm

It is difficult to maintain sperm in liquid storage for a long time, compared with permanent frozen storage in liquid nitrogen. Antioxidants have been reported to improve the quality and fertility of liquid-stored semen. In this study, we investigated whether antioxidants can extend the motility and fertility of frozen-thawed sperm in liquid storage. Frozen-thawed semen from one Japanese black bull (one ejaculate) was diluted in Tris-citrate-fructose (TCF) diluent with 10% (v/v) egg yolk to a sperm concentration of 1×107 spermmL−1. The antioxidants β-mercaptoethanol (βMe) and glutathione (GSH) were added independently, at various concentrations (0.1, 0.5, 1, and 5mM) to sperm suspensions, and these preparations were compared with Control (no added antioxidant). Sperm suspensions were packaged in centrifuge tubes and placed at 17°C in air and monitored daily until sperm motility had stopped (up to 14 days). Sperm motility was analysed by the Sperm Motility Analysis System (SMAS; Ditect Co. Ltd), and the percentage of progressively motile sperm (straight-line velocity (VSL) of &gt;25μm s−1; Grade A classified by WHO manual), compared with that recorded on Day 0 (100%), was determined each day. For evaluation of fertilizing ability, after incubation in liquid storage for 0, 3, 5, and 7 days, sperm were used for IVF with invitro-matured oocytes (30 oocytes per treatment, three replicates). Embryo development was recorded as the proportion of embryos that reached blastocyst by 8 days after IVF. Data for motility were analysed using one-way ANOVA with Tukey test, and embryo development using chi-squared test. A P-value&lt;0.05 was considered statistically significant. At 7 days, the percentage of progressively motile sperm was significantly higher for 0.5, 1, and 5mM βMe than for Control (30.8%, 48.1%, and 50.3%, vs. 0%, respectively). Treatments with 1 and 5mM βMe maintained some sperm progressive motility for 14 days (9.5% and 14.5%). Treatment with GSH showed the same trend at 7 days (32.2%, 36.3%, and 13.7% for 0.5, 1, and 5mM, vs. 0% for Control); 1 and 5mM GSH maintained sperm progressive motility over 10 days (24.8% and 4.4%). In both antioxidant treatments, embryo development was achieved with sperm stored for up to 5 days (Day 0 vs. Day 5 for 0.1mM βMe: 17.6% vs. 13.8%; for 1.0mM GSH: 26.0% vs. 6.7%; for Control: 17.6% vs. 0%). In this study, antioxidants extended both motility and fertility of frozen-thawed bovine sperm in liquid storage. This result suggests the possibility of application to AI using liquid-stored bovine semen.

Draft genome sequence data of Clostridium thermocellum PAL5 possessing high cellulose-degradation ability

Clostridium thermocellum is a potent cellulolytic bacterium. C. thermocellum strain PAL5, was derived from strain S14 that was isolated from bagasse paper sludge, possesses higher cellulose-degradation ability than representative strains ATCC27405 and DSM1313. In this work, we determined the draft genome sequence of C. thermocellum PAL5. Genomic DNA was used for whole-genome sequencing using the Illumina HiSeq 2500. We obtained 215 contigs of >200 bp (N50, 78,366 bp; mean length, 17,378 bp). The assembled data were subjected to the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline, and 3198 protein-coding sequences, 53 tRNA genes, and 4 rRNA genes were identified. The data are accessible at NCBI (the accession number SBHL00000000). Our data resource will facilitate further studies of efficient cellulose-degradation using C. thermocellum.

22 Vitrification of bovine embryo using antifreeze polyamino acid

Carboxylated poly-l-lysine (CPLL) is an ampholytic polymer compound and a polyamino acid with a known functional resemblance to antifreeze proteins. We previously reported that CPLL is an effective cryoprotectant for bovine cells, sperm, and slow-frozen embryos. In this study, we investigated CPLL as a cryoprotectant for vitrified bovine embryos. We developed bovine embryos in vitro and vitrified them at the blastocyst stage. Embryos were equilibrated (3min) and vitrified (1min). Vitrified embryos were cryopreserved in LN (Cryotop® device; Kitazato Corp., Tokyo, Japan) for at least 1 week, thawed with a 0.3M sucrose warming solution, and then cultured in a basal medium (Gibco® medium 199, Grand Island, NY, USA; supplemented with 100µM 2-mercaptoethanol, 10% fetal bovine serum, and antibiotics) at 38.5°C in a humidified atmosphere (5% CO2, 5% O2, 90% N2). We evaluated the embryos morphologically for survival and hatched rate at 0, 24, 48, and 72h post-thawing. In control, the equilibration solution (ES) consisted of 7.5% (vol/vol) dimethyl sulfoxide (DMSO) and 7.5% (vol/vol) ethylene glycol, and the vitrification solution (VS) consisted of 16.5% (vol/vol) DMSO and 16.5% (vol/vol) ethylene glycol and 0.5M sucrose. In this study, CPLL was added to ES and VS at various concentrations instead of DMSO. The CPLL was added at 16.5, 11.0, 5.5, and 2.2% (wt/vol) to VS; respectively, these solutions were named P16.5, P11.0, P5.5, and P2.2. The ES was used 45% CPLL of VS each. Embryos underwent the above procedure concurrently, with testing replicated at least 3 times. We evaluated 88, 34, 38, 44, and 28 embryos with each solution (control, P16.5, P11.0, P5.5, and P2.2, respectively). Results were analysed statistically with a chi-square test and residual analysis, regarding P&lt;0.05 as significant. Survival rates were significantly greater in P11.0 at 24h post-thawing (55.7% v. 89.5%; P&lt;0.05) and in P11.0 and P5.5 at 48h post-thawing (47.7% v. 78.9% and 47.7% v. 79.5%, respectively; P&lt;0.05) relative to controls but showed no significant differences at 0h post-thawing. Hatched rates were significantly greater in P11.0 and P5.5 through 72h post-thawing relative to controls (44.7% v. 22.7% and 52.3% v. 22.7%, respectively; P&lt;0.05). The CPLL improved post-thawing embryo survival and hatched rates when applied during vitrification, thus demonstrating cryoprotective effectiveness. We conclude that CPLL acts as a low-toxicity cryoprotectant for vitrified bovine embryos, and our results are consistent with previous reports of protective CPLL effects for cells and cell membranes.

Alterations of Candidatus Liberibacter asiaticus-Associated Microbiota Decrease Survival of Ca. L. asiaticus in in vitro Assays

Phloem-inhabiting bacterial phytopathogens often have smaller genomes than other bacterial phytopathogens. It is thought that they depend on both other phloem microbiota and phloem nutrients for colonization of the host. However, the mechanism underlying associations between phloem-inhabiting phytopathogens and other phloem microbiota are poorly understood. Here, we demonstrate that the survival of Candidatus Liberibacter asiaticus (CLas), a cause of huanglongbing (citrus greening disease), depends on interplay with a specific subset of CLas-associated microbiota. CLas was not susceptible to oxytetracycline in vitro. However, oxytetracycline treatment eliminated a particular sub-community dominated by the Comamonadaceae, Flavobacteriaceae, Microbacteriaceae, and Pseudomonadaceae, decreasing CLas survival. We speculate that CLas uses ecological services derived from CLas-associated microbiota to colonize the host and to construct a pathogen-associated community that stimulates disease development.

RNA sequence analysis data of Peronospora destructor maintained on onions

Peronospora destructor (Berk.) is an important biotrophic oomycete that causes downy mildew on onion (Allium Cepa L.) worldwide, especially in humid and temperate regions. The disease attacks bulb and seed production of onion, resulting in losses in yield and quality of bulbs. Epidemiological studies have increased our understanding and control of downy mildew on onion; however, little is known about the molecular aspects of P. destructor behavior during infection. Here, we isolated RNA from four samples of sporangia and sporangiophores of P. destructor, which were maintained by spore inoculation onto onions in a growth chamber. We then used an Ion PGM next generation sequencer to acquire and assemble the RNA sequences of P. destructor. By transcriptome shotgun assembly, we obtained 2335 contigs (N50, 884 nucleotides (nt); mean length, 881.6 nt). The data are accessible at NCBI (BioProject PRJNA391849). Our data resource will facilitate further studies of the molecular events during P. destructor infection.

Draft genome sequence of Colletotrichum sansevieriae Sa-1-2, the anthracnose pathogen of Sansevieria trifasciata

Colletotrichum sansevieriae is an ascomycete fungus causing anthracnose disease on plants in the genus Sansevieria. Here, we report the draft genome sequence of isolate Sa-1-2 of this fungus. The genome size is >51 Mb, and the assembly consists of 8647 contigs and contains 13,664 predicted protein-coding genes. Pathogenicity factors such as plant cell wall-degrading enzymes and effector proteins were also predicted. Additionally, the phylogenetic relationship of isolates from different Colletotrichum spp. was analyzed, revealing that the isolate belongs to a novel major clade consisting of species that infect succulent plants originating from Africa. The draft genome sequence has been deposited at GenBank under accession number NJHP00000000.

43 Cryopreservation of Bovine Sperm Using Antifreeze Polyamino-Acid

Carboxylated poly-l-lysine (CPLL), an ampholytic polymer compound, is reported to have a cryoprotective property similar to that of antifreeze proteins. We previously reported the effectiveness of CPLL as cryoprotective material for bovine sperm (43rd Annual Conference of International Embryo Technology Society, Austin, TX, USA; http://www.iets.org/2017/IETS_2017_Program_Book_FINAL.pdf). In this research, we investigated additional aspects of CPLL for bovine sperm. The conventional cryopreservation medium used for Control group consisted of 6.5% (v/v) glycerin, and the cryopreservation medium used for the CPLL group consisted of 3.25% (v/v) glycerin and 0.5% CPLL (w/v). In experiment 1, sperm motility was measured 1, 3, and 6 h after thawing. The post-thaw motility was assessed by using Sperm Motility Analysis System (DITECT Corp., Tokyo, Japan). The CPLL treatment yielded better motility rate at 6 h (Control v. CPLL; 23.7% v. 38.5%; P < 0.01), average path velocity (μm s−1) at 1 and 3 h (Control v. CPLL; 49.8 v. 57.7, 35.8 v. 42.8; P < 0.01), straight-line velocity (μm s−1) at 1 h (Control v. CPLL; 35.2 v. 45.7; P < 0.01), and curvilinear velocity (μm/s) at 1 and 3 h (Control v. CPLL; 93.7 v. 106.2, 59.9 v. 68.4; P < 0.01) than the Control. In experiment 2, sperm membrane integrity was assessed by using the LIVE/DEAD Sperm Viability Kit (Thermo Fisher Scientific K.K., Kanagawa, Japan). The CPLL group yielded greater sperm membrane integrity rate than control (Control v. CPLL; 49.6% v. 60.6%; P < 0.01). In experiment 3, AI was carried out on 111 cows (Control v. CPLL; 49 v. 62) and the conception rate of the CPLL group was significantly higher than that of the control group (53.1% v. 79.0%; P < 0.01). Previously, we reported the effectiveness of CPLL for bovine sperm. In this study, we clarified how CPLL works to improve the conception rate of AI: CPLL maintains post-thaw motility and protects the sperm membrane. These results suggest that CPLL has potential as a new cryoprotective material for bovine sperm.

Monozygotic twins discordant for primary aldosteronism: a case report

This corrects the article DOI: 10.1038/jhh.2017.41.

The hypothalamic regulation of metabolic adaptations to exercise

Our modern lifestyle is characterised by easy access to nutrient dense foods combined with limited physical activity. A sedentary lifestyle is one of several factors that have contributed to the global obesity epidemic and it also predisposes to chronic illnesses such as diabetes and cardiovascular disease. Although many studies have focused on the benefits of exercise in peripheral tissues, the contributions of the central nervous system to these exercise-induced metabolic adaptations are relatively unknown. The present review highlights the role of the ventromedial hypothalamus in regulating the metabolic response to exercise.

Ectopic accumulation of linalool confers resistance to Xanthomonas citri subsp. citri in transgenic sweet orange plants

In order to clarify whether high linalool content in citrus leaves alone induces strong field resistance to citrus canker caused by Xanthomonas citri subsp. citri (Xcc), and to assess whether this trait can be transferred to a citrus type highly sensitive to the bacterium, transgenic 'Hamlin' sweet orange (Citrus sinensis L. Osbeck) plants over-expressing a linalool synthase gene (CuSTS3-1) were generated. Transgenic lines (LIL) with the highest linalool content showed strong resistance to citrus canker when spray inoculated with the bacterium. In LIL plants inoculated by wounding (multiple-needle inoculation), the linalool level was correlated with the repression of the bacterial titer and up-regulation of defense-related genes. The exogenous application of salicylic acid, methyl jasmonate or linalool triggered responses similar to those constitutively induced in LIL plants. The linalool content in Ponkan mandarin leaves was significantly higher than that of leaves from six other representative citrus genotypes with different susceptibilities to Xcc. We propose that linalool-mediated resistance might be unique to citrus tissues accumulating large amounts of volatile organic compounds in oil cells. Linalool might act not only as a direct antibacterial agent, but also as a signal molecule involved in triggering a non-host resistance response against Xcc.

52 CRYOPRESERVATION OF BOVINE SOMATIC CELL USING ANTIFREEZE POLYAMINO-ACID (CARBOXYLATED POLY-L-LYSINE)

Cryopreservation is used for long-term preservation of biological materials containing cell and tissue, somatic cells are important to commercial application in gene bank and medical engineer. For cell cryopreservation, dimethyl sulfoxide (DMSO) have been used widely as cryoprotective material for long time. Carboxylated poly-l-lysine (CPLL) is an ampholytic polymer compound obtained by converting 65% amino groups to carboxyl groups after synthesising ε-poly-l-lysine aqueous solution and succinic anhydride. It is reported that the addition of CPLL into cryopreservation medium improves the post-thaw survival rate of murine L929 cells, human induced pluripotent stem cells and murine embryo. In this research, the effectiveness of CPLL as bovine somatic cell cryoprotective material was examined. In experiment 1, using bovine fibroblast cells from skin, the cryopreservation media were prepared as follows: 10% (vol/vol) DMSO, 5% (vol/vol) DMSO + 5% (wt/vol) CPLL, 5% (wt/vol) CPLL, 7.5% (wt/vol) CPLL, 10% (wt/vol) CPLL and 20% (wt/vol) CPLL were dissolved in DMEM and pH was adjusted to 7.4. Cells were resuspended in 1 mL of cryopreservation medium at a cell density of 5 × 105 and stored in a −80°C freezer. After storage for at least 1 wk, cells were thawed. The 5% CPLL showed significantly higher post-thaw survival rate than 10% DMSO (96.5% v. 86.7%; P < 0.05), and 7.5% CPLL and 20% CPLL showed significantly higher proliferation rates than 10% DMSO at 72 h after thawing (10% DMSO v. 7.5% CPLL v. 20% CPLL ; 99.4% v. 173.6% v. 207.4%; P < 0.05). Although it is necessary to remove the cryoprotective material after thawing, the proliferation rate at 72 h after thawing of 5% CPLL and 10% CPLL without removal of cryoprotective material were significantly higher than that when removing cryoprotective material (111.2% v. 269.6%, 113.0% v. 210.0%). In addition, there was no difference between the removal treatment of CPLL and the NOT removal treatment of CPLL at the thawing. In experiment 2, using bovine cumulus cells, the cryopreservation media were prepared as follows: 10% (vol/vol) DMSO, 5% (vol/vol) DMSO + 5% (wt/vol) CPLL, 5% (wt/vol) CPLL, 10% (wt/vol) CPLL, 20% (wt/vol) CPLL, 25% (wt/vol) CPLL, and 30% (wt/vol) CPLL were dissolved in DMEM and other conditions were the same as experiment 1. There was no significant difference for post-thaw survival rate (93.7, 91.8, 89.2, 89.2, 95.3, 91.6, and 90.2%). At 72 h after thawing, 10% DMSO, 5% DMSO + 5% CPLL and 25% CPLL showed higher proliferation rate (10% DMSO v. 5% DMSO + 5% CPLL v. 25% CPLL; 258.4% v. 281.4% v. 257.4%). The significant differences in survival rate were determined by chi-squared test, and in proliferation were determined by ANOVA. In bovine somatic cells, it was possible to cryopreserve cells using CPLL without DMSO. The cryoprotective effect of CPLL is equal or superior to that of DMSO, the conventional cryoprotective material. Further, when using CPLL, it was possible to culture without removing the cryopreservation medium after thawing. These results suggest that CPLL has promise as a new cryoprotective material for bovine somatic cells.

47 CRYOPRESERVATION OF BOVINE GERM CELL USING ANTIFREEZE POLYAMINO-ACID (CARBOXYLATED POLY-L-LYSINE)

Carboxylated poly-l-lysine (CPLL) is an ampholytic polymer compound, and it is obtained by converting 65% amino groups to carboxyl groups after synthesising ε-poly-l-lysine aqueous solution and succinic anhydride. CPLL has cryoprotective property similar to antifreeze protein, and addition of CPLL into cryopreservation medium improves the post-thaw survival rate of cells and embryos. In this research, we examined the effectiveness of CPLL as a bovine germ cell cryoprotective material. In experiment 1 (in sperm), the conventional cryopreservation medium used for control group was consisted of 6.5% (vol/vol) glycerin, and the cryopreservation medium used for CPLL group was consisted of 3.25% (vol/vol) glycerin and 0.5% CPLL (wt/vol). The post-thaw survival and motility were assessed by using Sperm Motility Analysis System (DITECT Corp., Tokyo, Japan). There was no significant difference for post-thaw survival rate and motility (control v. CPLL; 98.8% v. 96.6% and 69.7% v. 62.2%, respectively). Artificial insemination was carried out in 65 cows (control v. CPLL; 34 v. 31), and the conception rate of the CPLL group was higher than that of the control group (80.6% v. 67.6%; P = 0.23). In experiment 2 (embryos), the conventional cryopreservation medium used for control group was consisted of 5% (vol/vol) ethylene glycol and 6% (vol/vol) propylene glycol in PBS. In the CPLL group, 7% (wt/vol) CPLL was added to the conventional medium. In vitro fertilization embryos were cryopreserved at Day 7 and Day 8. There was no significant difference in survival rate at 0, 24, and 48 h and hatched rate until 72 h after thawing (control v. CPLL: 93.6% v. 93.2%, 69.0% v. 64.7%, 56.1% v. 56.3%, 12.9% v. 10.2%, respectively). Embryos obtained by superovulation treatment and in vivo fertilization at Day 7 were cryopreserved using above 2 media, and transferred non-surgically into synchronized recipient cows (1 embryo per animal). Embryo transfer (ET) was carried out in 81 cows (control v. CPLL: 31 v. 50), and recipients were diagnosed for pregnancy ultrasonically 50 days after embryo transfer. Conception rate of CPLL group was higher than control group (50.0% v. 29.0%; P = 0.063). In both experiments, the significant differences between control group and CPLL group were determined by chi-squared test. The effectiveness of CPLL in cells and embryos has been reported; however, there is no report using CPLL in bovine germ cells. In this research, CPLL improved the conception rate of AI and ET, probably due to its low toxicity and protection of the cell membrane. These results suggest that CPLL is available as a new cryoprotective material for bovine sperm and embryo in slow freezing methods.

Structure determination of molecules in an alignment laser field by femtosecond photoelectron diffraction using an X-ray free-electron laser

We have successfully determined the internuclear distance of I₂ molecules in an alignment laser field by applying our molecular structure determination methodology to an I 2p X-ray photoelectron diffraction profile observed with femtosecond X-ray free electron laser pulses. Using this methodology, we have found that the internuclear distance of the sample I₂ molecules in an alignment Nd:YAG laser field of 6 × 10¹¹ W/cm² is elongated by from 0.18 to 0.30 Å “in average” relatively to the equilibrium internuclear distance of 2.666 Å. Thus, the present experiment constitutes a critical step towards the goal of femtosecond imaging of chemical reactions and opens a new direction for the study of ultrafast chemical reaction in the gas phase.

Nucleotide sequences of Japanese isolates of citrus vein enation virus

The genomic sequences of five Japanese isolates of citrus vein enation virus (CVEV) isolates that induce vein enation were determined and compared with that of the Spanish isolate VE-1. The nucleotide sequences of all Japanese isolates were 5,983 nt in length. The genomic RNA of Japanese isolates had five potential open reading frames (ORF 0, ORF 1, ORF 2, ORF 3, and ORF 5) in the positive-sense strand. The nucleotide sequence identity among the Japanese isolates and Spanish isolate VE-1 ranged from 98.0% to 99.8%. Comparison of the partial amino acid sequences of ten Japanese isolates and three Spanish isolates suggested that four amino acid residues, at positions of 83, 104, and 113 in ORF 2 and position 41 in ORF 5, might be unique to some Japanese isolates.

Genome analysis of the kiwifruit canker pathogen Pseudomonas syringae pv. actinidiae biovar 5

Pseudomonas syringae pv. actinidiae (Psa) is a destructive pathogen of kiwifruit bacterial canker disease, causing severe economic losses to kiwifruit industry worldwide. Biovar 5 is the most recently reported biovar of Psa, and is found in only a local area of Japan at present. There is not much information of genetic characteristics of biovar 5. Thus, the genome of biovar 5 was sequenced and analyzed to clarify its detailed genetic characteristics. Here, the genomes of strain MAFF 212056 and MAFF 212061 of biovar 5 were estimated to be about 6.3 Mbp and 6.5 Mbp, respectively, and their phylogenetic positions were proved to be near that of biovar 2 in the phylogenetic tree. However, it was confirmed that biovar 5 had neither the coronatine biosynthetic genes conserved in biovar 2, its phylogenetic neighbor, nor the phaseolotoxin biosynthetic genes conserved in biovar 1, Japanese native pathogen. In addition, 45 genes of type III secreted effectors were identified in biovar 5 genomes, showing that their composition is different from that in the other biovars. Moreover, some biovar 5-specific regions were identified. Then, biovar 5-specific PCR primers for targeting these regions were designed, and proved to be applicable for detecting biovar 5 specifically.

Operative Results and Clinical Features of Chronic Stanford Type B Aortic Dissection: Examination of 234 Patients Over 6 Years

OBJECTIVE/BACKGROUND

Recently, the indications for thoracic endovascular aortic repair (TEVAR) have been expanding, and the applicability of TEVAR for acute type B aortic dissection (TBAD) is proposed with regard to the high mortality of open surgery for chronic TBAD. TEVAR in the acute phase may lead to remodeling of the false lumen (FL), but it is controversial whether it completely resolves the aortic expansion in the chronic phase. In this study, operative results and the relationship between FL status and the time before surgical intervention were retrospectively analyzed.

METHODS

From January 2008 to September 2013, 234 patients underwent open surgery for chronic TBAD. Most patients were on left heart bypass. By considering Japanese aortic disease treatment guidelines and the smaller physique of Japanese patients, operative indications were aneurysm >50 mm in diameter or rapid aneurysm enlargement of >5 mm in a 6 month period.

RESULTS

In 180 cases, the FL was patent. The mean interval between onset of TBAD and operation was 61 ± 54 months. There was no significant difference between patients in the patent FL group and those in the thrombosed FL group (p = .44). Mean ratio of FL diameter to maximum aortic diameter (FL/AD) was 0.64 ± 0.21. There was no correlation between FL and AD before the operation (r = .12). Descending thoracic aortic replacement (DTAR) was performed in 127 cases and thoracic ascending aortic replacement (TAAR) in 107 cases (Crawford type I, n = 9; Crawford type II, n = 65; Crawford type III and IV, n = 22, respectively; Safi type V, n = 11). The overall operative mortality was 6.8%: 3.9% (5/127) for DTAR and 10.3% (11/107) for TAAR. The three year survival was 86.7, and the freedom from re-intervention rate was 97.0%.

CONCLUSION

Enlargement of uncomplicated TBAD in the chronic phase was poorly related to FL status and the results of open repair have improved. However, further prospective study is necessary.

Photoelectron diffraction from laser-aligned molecules with X-ray free-electron laser pulses

We report on the measurement of deep inner-shell 2p X-ray photoelectron diffraction (XPD) patterns from laser-aligned I₂ molecules using X-ray free-electron laser (XFEL) pulses. The XPD patterns of the I₂ molecules, aligned parallel to the polarization vector of the XFEL, were well matched with our theoretical calculations. Further, we propose a criterion for applying our molecular-structure-determination methodology to the experimental XPD data. In turn, we have demonstrated that this approach is a significant step toward the time-resolved imaging of molecular structures.

Development of soybean certified reference material for pesticide residue analysis

A soybean certified reference material for pesticide residue analysis was developed by the National Metrology Institute of Japan. Three organophosphorus (diazinon, fenitrothion, chlorphyrifos) and one pyrethroid (permethrin) pesticides were sprayed on soybeans three times before harvest. These soybeans were freeze pulverized, homogenized, bottled, and sterilized by γ-irradiation to prepare the candidate material. Three isotope-dilution mass spectrometric methods that varied in terms of the solvents used for extraction of the target pesticides, the clean-up procedure, and the injection techniques and columns used for quantification via gas chromatography/mass spectrometry were applied to the characterization. Each target pesticide was quantified by two of these analytical methods, and the results were in good agreement. Homogeneity and stability assessment of the material demonstrated that the relative standard uncertainties due to the inhomogeneity and the instability for an expiry date of 55 months were 1.89-4.00% and 6.65-11.5%, respectively. The certified pesticide concentrations with expanded uncertainties (coverage factor k=2, approximate 95% confidence interval) calculated using the results of the characterization and the homogeneity and stability assessment were 21.7 ± 3.2 μg/kg for diazinon, 88 ± 21 μg/kg for fenitrothion, 11.1 ± 3.2 μg/kg for chlorpyrifos, and 20.1 ± 4.3 μg/kg for permethrin (as the sum of the constituent isomers).