Functional lipid pairs as building blocks of phase-separated membranes.

Biological membranes exhibit a great deal of compositional and phase heterogeneity due to hundreds of chemically distinct components. As a result, phase separation processes in cell membranes are extremely difficult to study, especially at the molecular level. It is currently believed that the lateral membrane heterogeneity and the formation of domains, or rafts, are driven by lipid-lipid and lipid-protein interactions. Nevertheless, the underlying mechanisms regulating membrane heterogeneity remain poorly understood. In the present work, we combine inelastic X-ray scattering with molecular dynamics simulations to provide direct evidence for the existence of strongly coupled transient lipid pairs. These lipid pairs manifest themselves experimentally through optical vibrational (a.k.a. phononic) modes observed in binary (1,2-dipalmitoyl-sn-glycero-3-phosphocholine [DPPC]-cholesterol) and ternary (DPPC-1,2-dioleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-glycero-3-phosphocholine [DOPC/POPC]-cholesterol) systems. The existence of a phononic gap in these vibrational modes is a direct result of the finite size of patches formed by these lipid pairs. The observation of lipid pairs provides a spatial (subnanometer) and temporal (subnanosecond) window into the lipid-lipid interactions in complex mixtures of saturated/unsaturated lipids and cholesterol. Our findings represent a step toward understanding the lateral organization and dynamics of membrane domains using a well-validated probe with a high spatial and temporal resolution.

Short-Range Nematic Fluctuations in Sr_{1-x}Na_{x}Fe_{2}As_{2} Superconductors.

Interactions between nematic fluctuations, magnetic order and superconductivity are central to the physics of iron-based superconductors. Here we report on in-plane transverse acoustic phonons in hole-doped Sr_{1-x}Na_{x}Fe_{2}As_{2} measured via inelastic x-ray scattering, and extract both the nematic susceptibility and the nematic correlation length. By a self-contained method of analysis, for the underdoped (x=0.36) sample, which harbors a magnetically ordered tetragonal phase, we find it hosts a short nematic correlation length ξ∼10 Å and a large nematic susceptibility χ_{nem}. The optimal-doped (x=0.55) sample exhibits weaker phonon softening effects, indicative of both reduced ξ and χ_{nem}. Our results suggest short-range nematic fluctuations may favor superconductivity, placing emphasis on the nematic correlation length for understanding the iron-based superconductors.

Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume.

Chinese liquorice/licorice (Glycyrrhiza uralensis) is a leguminous plant species whose roots and rhizomes have been widely used as a herbal medicine and natural sweetener. Whole-genome sequencing is essential for gene discovery studies and molecular breeding in liquorice. Here, we report a draft assembly of the approximately 379-Mb whole-genome sequence of strain 308-19 of G. uralensis; this assembly contains 34 445 predicted protein-coding genes. Comparative analyses suggested well-conserved genomic components and collinearity of gene loci (synteny) between the genome of liquorice and those of other legumes such as Medicago and chickpea. We observed that three genes involved in isoflavonoid biosynthesis, namely, 2-hydroxyisoflavanone synthase (CYP93C), 2,7,4'-trihydroxyisoflavanone 4'-O-methyltransferase/isoflavone 4'-O-methyltransferase (HI4OMT) and isoflavone-7-O-methyltransferase (7-IOMT) formed a cluster on the scaffold of the liquorice genome and showed conserved microsynteny with Medicago and chickpea. Based on the liquorice genome annotation, we predicted genes in the P450 and UDP-dependent glycosyltransferase (UGT) superfamilies, some of which are involved in triterpenoid saponin biosynthesis, and characterised their gene expression with the reference genome sequence. The genome sequencing and its annotations provide an essential resource for liquorice improvement through molecular breeding and the discovery of useful genes for engineering bioactive components through synthetic biology approaches.

Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering.

We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298-220 K). We interpret this change in terms of the dynamic transition previously discussed using other probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.

Inelastic X-ray scattering with 0.75 meV resolution at 25.7 keV using a temperature-gradient analyzer.

The use of temperature-gradient analyzers for non-resonant high-resolution inelastic X-ray scattering is investigated. The gradient compensates for geometrical broadening of the energy resolution by adjusting the lattice spacing of the analyzer crystal. Applying a ∼ 12 mK temperature gradient across a 9.5 cm analyzer, resolutions of 0.75 (2) meV FWHM at 25.7 keV for Si(13 13 13) and 1.25(2) meV at 21.7 keV for Si(11 11 11) were measured, while retaining large (250 mm) clearance between the sample position and detector, and reasonable (9.3 mrad × 8.8 mrad) analyzer acceptance. The temperature control and stability are discussed.

Inelastic X-ray scattering of a transition-metal complex (FeCl4(-)): vibrational spectroscopy for all normal modes.

The tetraethylammonium salt of the transition-metal complex FeCl4(-) has been examined using inelastic X-ray scattering (IXS) with 1.5 meV resolution (12 cm(-1)) at 21.747 keV. This sample serves as a feasibility test for more elaborate transition-metal complexes. The IXS spectra were compared with previously recorded IR, Raman, and nuclear resonant vibrational spectroscopy (NRVS) spectra, revealing the same normal modes but with less strict selection rules. Calculations with a previously derived Urey-Bradley force field were used to simulate the expected Q and orientation dependence of the IXS intensities. The relative merits of IXS, compared to other photon-based vibrational spectroscopies such as NRVS, Raman, and IR, are discussed.

Communication: collective dynamics of room-temperature ionic liquids and their Li ion solutions studied by high-resolution inelastic X-ray scattering.

High-resolution inelastic X-ray scattering (IXS) measurements were performed for room-temperature ionic liquids (ILs) of 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide and bis(fluorosulfonyl)amide, [C2mIm(+)][TFSA(-)] and [C2mIm(+)][FSA(-)], respectively, at ambient temperature. The observed spectra as a function of Q of 1.4-6 nm(-1) can be ascribed to quasi-elastic and inelastic scatterings, so that they are well represented with the fitting by using the Lorentz and the damped harmonic oscillator model functions to yield the dynamic structure factors. It was found in the intermediate scattering function, F(Q, t) that both ILs show the relaxation at t < 10 ps. The IXS measurements were also made on [C2mIm(+)][TFSA(-)] and [C2mIm(+)][FSA(-)] solutions dissolving Li salt. It is suggested that the adding of Li salt to IL significantly prolongs the relaxation time.

Discriminative phytoalexin accumulation in Lotus japonicus against symbiotic and non-symbiotic microorganisms and related chemical signals.

The phytoalexin response of Lotus japonicus seedlings to selected microbes and chemical signals was analyzed. The symbiotic rhizobium induced vestitol production weakly, while non-symbiotic rhizobia and potential pathogens led to increases in its accumulation. Whereas chitin-related molecules were ineffective, a flagellin-derived peptide not of symbiont origin induced phytoalexin production, indicating discriminative antibiotic production by the plant host.

Phonon dispersion curves in the type-I crystalline and molten clathrate compound Eu8Ga16Ge30.

The dynamic structure factorS(Q,E), whereQandEare momentum and energy transfer, respectively, has been measured for liquid Eu8Ga16Ge30(EGG), using inelastic x-ray scattering. The excitation energy of the longitudinal acoustic mode in the liquid was scaled to that in liquid Ba8Ga16Sn30(BGS) with the effective mass. This result means that the local structure in both liquids are similar. The longitudinal acoustic excitation energy of type-I clathrate compound EGG disperses faster than that in the liquid, suggesting that the interatomic force is weakened on melting. The lower energy excitation was observed in both liquid EGG and liquid BGS. In comparison with the longitudinal phonon dispersion in crystalline clathrate compound EGG obtained by density functional theory-based calculations, the lower energy in the liquid was found to be near the optical mode energy. The result indicates that the lower energy mode arises from the relative motion between Eu and (Ga, Ge) atoms.

Use of RAPD analysis to assess the threat of interspecific hybridization to the critically endangered Polemonium kiushianum in Japan.

Polemonium kiushianum is a critically endangered species of which only eight populations exist in semi-natural grasslands of the Mt. Aso area of Kyushu, Japan. Habitat modification and the risk of hybridization with non-indigenous horticultural congeners, such as P. caeruleum subsp. caeruleum and P. caeruleum subsp. yezoense var. yezoense, pose increasing threats to P. kiushianum. To develop a DNA marker that distinguishes P. kiushianum from other Polemonium species, we performed random amplified polymorphic DNA (RAPD) analysis and selected an approximately 500-bp fragment generated by the OPB06 RAPD primer. In addition, we designed a primer pair, H11F/R, based on the nucleotide sequences of the fragments derived from P. caeruleum subsp. caeruleum and P. caeruleum subsp. yezoense var. yezoense. The results with the H11F/R primers indicated that most extant P. kiushianum plants in natural populations are not genetically contaminated by hybridization with non-indigenous horticultural species.

Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis.

Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes' evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

Alterations in smoking habits are associated with acute eosinophilic pneumonia.

BACKGROUND: Acute eosinophilic pneumonia (AEP) is characterized by a febrile illness, diffuse pulmonary infiltrates, and pulmonary eosinophilia. The etiology of AEP remains unknown, but several studies have proposed a relationship between cigarette smoking and AEP. However, most studies showing this possibility are single-case reports, and cigarette smoke has not been fully validated as a causative agent of AEP in a large series of patients. The present study was conducted to clarify the etiologic role of cigarette smoking in AEP, with special reference to alterations in smoking habits. METHODS: We took a detailed history of smoking habits before AEP onset in 33 patients with AEP, and performed a cigarette smoke provocation test. RESULTS: Of our AEP patients, all but one (97%) were current smokers. Interestingly, 21 of these were new-onset smokers, and 2 had restarted smoking after a 1- to 2-year cessation of smoking. The duration between starting smoking and AEP onset was within 1 month (0.67 +/- 0.53 months). Additionally, six of the remaining smokers had increased the quantity of cigarettes smoked daily, fourfold to fivefold, mostly within the month before AEP onset (0.81 +/- 0.58 months). Only three smokers had not changed their smoking habits before AEP onset. Cigarette smoke provocation tests revealed positive results in all nine patients tested. CONCLUSION: These data suggest that recent alterations in smoking habits, not only beginning to smoke, but also restarting to smoke and increasing daily smoking doses, are associated with the development of AEP.

[Acute respiratory failure due to pneumocystis pneumonia successfully treated with combined use of sivelestat sodium hydrate].

A 22-year-old man was admitted to our hospital with fever, cough and dyspnea. His chest radiograph showed diffuse ground-glass attenuation in both lung fields. Arterial blood gas analysis showed hypoxemia (PaO2 28.7 Torr breathing room air) and he required mechanical ventilation within 6 hours after admission. Gomori methenamine silver (GMS) stain of the bronchoalveolar lavage (BAL) fluid smear showed round and indented organisms, and polymerase chain reaction revealed pneumocystis jirovecii in the BAL fluid. The HIV antibody was positive and peripheral blood CD4-positive lymphocytes decreased to 4.0%. Pneumocystis pneumonia complicated with acquired immunodeficiency syndrome (AIDS) was diagnosed. There was no four-fold rise in screen viral titers. We treated him with antibiotics, trimethoprim-sulfamethoxazole, ganciclovir, fos-fluconazole, steroid pulse therapy and sivelestat sodium hydrate. Respiratory failure was relieved within 5 days following treatment. The percentage of neutrophils in the BAL fluid was elevated (44.6%). Neutrophil elastase on admission was increased and improved to the normal range after treatment. Sivelestat sodium hydrate is an anti-neutrophil elastase inhibitor and may be one of the treatment options for acute respiratory failure due to pneumocystis pneumonia in AIDS patients.

Traditional knowledge of wild edible plants with special emphasis on medicinal uses in Southern Shan State, Myanmar.

BACKGROUND: Myanmar is one of the hotspots of biodiversity and is a rapidly developing country. Performing floristic research in Myanmar is an urgent issue, and ethnobotanical studies of wild edible plants (WEPs) will provide new information on natural plant resources. METHOD: Ethnobotanical data were collected in three villages with different historical backgrounds in Southern Shan State, Myanmar. A total of 19 key informants were interviewed, and specimens were collected in the fields with the participation of key informants in June-July 2015. Group discussions were organized during 2016 and 2017 to reinforce the information on use of WEPs. DNA barcoding was used to facilitate species identification. RESULTS: A total of 83 species from 44 families of angiosperms were recorded as WEPs. Most of the species were used as wild vegetables (47 species), followed by fruits and nuts (31 species). Eighteen WEPs were consumed as medicinal foods. Differences in use of WEPs between the communities of the villages were observed. The age class of 30-39 years was more familiar with the environments where they could collect WEPs and had more knowledge of WEPs than did the older groups. The use of Elaeocarpus floribundus as an edible oil is a very interesting tradition. CONCLUSION: WEPs play an important role in the livelihood of local communities. The indigenous society has maintained traditional knowledge of the WEPs. Historical background, land use system and surrounding vegetation could have effects on the variation in the traditional uses of WEPs. Increasing awareness of the importance of WEPs will encourage the conservation of traditional knowledge of indigenous populations.

Chromosomal study of lettuce and its allied species (Lactuca spp., Asteraceae) by means of karyotype analysis and fluorescence in situ hybridization.

In this study, in addition to the karyotype analysis, the chromosomal distributions of 5 S and 18 S rDNAs, and the Arabidopsis-type (T3AG3) telomeric sequences were detected by means of fluorescence in situ hybridization (FISH) to promote the information of chromosomal organization and evolution in the cultivated lettuce and its wild relatives, L. sativa, L. serriola, L. saligna and L. virosa. The karyotype analysis revealed the dissimilarity between L. virosa and the remaining species. In all four Lactuca species studied, one 5 S rDNA and two 18 S rDNA loci were detected. The simultaneous FISH of 5 S and 18 S rDNAs revealed that both rDNA loci of L. sativa, L. serriola and L. saligna were identical, however, that of L. virosa was different from the other species. These analyses indicate the closer relationships between L. sativa/L. serriola and L. saligna rather than L. virosa. Arabidopsis-type telomeric sequences were detected at both ends of their chromatids of all chromosomes not in the other regions. This observation suggests the lack of telomere-mediated chromosomal rearrangements among the Lactuca chromosomes.

Pressure dependence of transverse acoustic phonon energy in ferropericlase across the spin transition.

We investigated transverse acoustic (TA) phonons in iron-bearing magnesium oxide (ferropericlase) up to 56 GPa using inelastic x-ray scattering (IXS). The results show that the energy of the TA phonon far from the Brillouin zone center suddenly increases with increasing pressure above the spin transition pressure of ferropericlase. Ab initio calculations revealed that the TA phonon energy far from the Brillouin zone center is higher in the low-spin state than in the high spin state; that the TA phonon energy depend weakly on pressure; and that the energy gap between the TA and the lowest-energy-optic phonons is much narrower in the low-spin state than in the high-spin state. This allows us to conclude that the anomalous behavior of the TA mode in the present experiments is the result of gap narrowing due to the spin transition and explains contradictory results in previous experimental studies.

Catalytic specificity of pea O-methyltransferases suggests gene duplication for (+)-pisatin biosynthesis.

S-adenosyl-l-methionine: 2-hydroxyisoflavanone 4'-O-methyltransferase (HI4'OMT) methylates 2,7, 4'-trihydroxyisoflavanone to produce formononetin, an essential intermediate in the synthesis of isoflavonoids with methoxy or methylenedioxy groups at carbon 4' (isoflavone numbering). HI4'OMT is highly similar (83% amino acid identity) to (+)-6a-hydroxymaackiain 3-O-methyltransferase (HMM), which catalyzes the last step of (+)-pisatin biosynthesis in pea. Pea contains two linked copies of HMM with 96% amino acid identity. In this report, the catalytic activities of the licorice HI4'OMT protein and of extracts of Escherichia coli containing the pea HMM1 or HMM2 protein are compared on 2,7,4'-trihydroxyisoflavanone and enantiomers of 6a-hydroxymaackiain. All these enzymes produced radiolabelled 2,7-dihydroxy-4'-methoxyisoflavanone or (+)-pisatin from 2,7,4'-trihydroxyisoflavanone or (+)-6a-hydroxymaakiain when incubated with [methyl-(14)C]-S-adenosyl-l-methionine. No product was detected when (-)-6a-hydroxymaackiain was used as the substrate. HI4'OMT and HMM1 showed efficiencies (relative V(max)/K(m)) for the methylation of 2,7,4'-trihydroxyisoflavanone 20 and 4 times higher than for the methylation of (+)-6a-hydroxymaackiain, respectively. In contrast, HMM2 had a higher V(max) and lower K(m) on (+)-6a-hydroxymaackiain, and had a 67-fold higher efficiency for the methylation of (+)-6a-hydroxymaackiain than that for 2,7,4'-trihydroxyisoflavanone. Among the 15 sites at which HMM1 and HMM2 have different amino acid residues, 11 of the residues in HMM1 are the same as found in HI4'OMTs from three plant species. Modeling of the HMM proteins identified three or four putative active site residues responsible for their different substrate preferences. It is proposed that HMM1 is the pea HI4'OMT and that HMM2 evolved by the duplication of a gene encoding a general biosynthetic enzyme (HI4'OMT).

[Two cases of acute respiratory failure due to idiopathic interstitial pneumonia successfully treated with sivelestat sodium hydrate and steroid therapy].

We encountered two patients with clinically diagnosed idiopathic interstitial pneumonia with acute respiratory distress syndrome (ARDS). Both patients required mechanical ventilation within 24 hours after admission. We managed these patients using lower tidal volume ventilation (tidal volume: 5-6 ml/kg), antibiotics, sivelestat sodium hydrate and steroid pulse therapy followed by oral prednisolone therapy. Respiratory failure was relieved within 2 weeks following treatment There was no four-fold rise in screen viral titers and screening investigations of autoantibodies were negative. Based on these findings, we diagnosed these cases as having acute interstitial pneumonia (AIP). AIP represents a small subset of patients with ARDS without any associated or predisposing factor. Sivelestat sodium hydrate is an anti-neutrophil elastase inhibitor and is used for the treatment of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS). Therefore, sivelestat sodium hydrate may be one of the treatment options for acute respiratory failure due to idiopathic interstitial pneumonia.

Effect of cation substitution on bridgmanite elasticity: A key to interpret seismic anomalies in the lower mantle.

Seismological observations show that, in some regions of the lower mantle, an increase in bulk sound velocity, interestingly, occurs in the same volume where there is a decrease in shear velocity. We show that this anti-correlated behavior occurs on cation substitution in bridgmanite by making single crystal elasticity measurements of MgSiO3 and (Mg,Fe,Al)(Si,Al)O3 using inelastic x-ray scattering in the ambient conditions. Cation substitution of ferrous iron and aluminum may explain large low shear velocity provinces in the lower mantle.

Optimum dose of LH-RH analogue Fertirelin Acetate for the induction of superovulation in mice.

The optimum dose for establishing superovulation in mice of Fertirelin Acetate (FA), an LH-RH analogue, was examined. Mice were subcutaneously injected with 5 IU of hCG at 17:00 (Day 0), and with various doses of FA (0.001 to 1.0 microg) five times at 4 h intervals on and after 22:00 on Day 0. To induce ovulation, 5 IU of hCG was again injected subcutaneously at 17:00 on Day 2. In the groups administered with doses ranging from 0.01 to 0.5 microg of FA, the number of ovulated eggs was significantly (p<0.05) larger than in the control group (12.9 +/- 5.9). The greatest number of ovulated eggs (22.6 +/- 7.3) was obtained in the group administered with 0.025 microg of FA. The results indicate that the effective dose of LH-RH analogue, FA, is between 0.1 and 0.5 microg for superovulation induction in mice.