Structure,variation, and assembly of the root-associated microbiomes of rice

Plants depend upon beneficial interactions between roots and microbes for nutrient availability, growth promotion, and disease suppression. High-throughput sequencing approaches have provided recent insights into root microbiomes, but our current understanding is still limited relative to animal microbiomes. Here we present a detailed characterization of the root-associated microbiomes of the crop plant rice by deep sequencing, using plants grown under controlled conditions as well as field cultivation at multiple sites. The spatial resolution of the study distinguished three root-associated compartments, the endosphere (root interior), rhizoplane (root surface), and rhizosphere (soil close to the root surface), each of which was found to harbor a distinct microbiome. Under controlled greenhouse conditions, microbiome composition varied with soil source and genotype. In field conditions, geographical location and cultivation practice, namely organic vs. conventional, were factors contributing to microbiome variation. Rice cultivation is a major source of global methane emissions, and methanogenic archaea could be detected in all spatial compartments of field-grown rice. The depth and scale of this study were used to build coabundance networks that revealed potential microbial consortia, some of which were involved in methane cycling. Dynamic changes observed during microbiome acquisition, as well as steady-state compositions of spatial compartments, support a multistep model for root microbiome assembly from soil wherein the rhizoplane plays a selective gating role. Similarities in the distribution of phyla in the root microbiomes of rice and other plants suggest that conclusions derived from this study might be generally applicable to land plants.Land plants grow in soil, placing them in direct proximity to a high abundance of microbial diversity (1). Plants and microbes have both adapted to use their close association for their mutual benefit. Critical nutrients are converted to more usable forms by microbes before assimilation by plants (2–4). In turn, bacteria in the rhizosphere receive carbon metabolites from the plant through root exudates (5). Beneficial soil microbes also contribute to pathogen resistance, water retention, and synthesis of growth-promoting hormones (6–8).Recent studies have used high-throughput sequencing to provide new insights into the bacterial composition and organization of different plant microbiomes, including Arabidopsis, Populus, and maize (9–14). Detailed characterization of the core root microbiome of Arabidopsis (9–11) showed that the dominant phyla inside the root (the endosphere) are much less diverse than the phyla in the soil around the root (the rhizosphere), and a potential core root microbiome could be identified. In Arabidopsis, the endophytic microbiome exhibits some genotype-dependent variation within the species and an increased variation when other related species are examined (9–11). A recent study in maize examined microbiome variation across many different inbred lines at different sites and found a large variation arising from geographical location between three different states in the United States and a relatively smaller dependence on the genotype (12). Although the microbiomes examined in the maize study consisted of combined rhizospheric and endospheric microbes (12), a study in poplar found that the variation between locations in two different states affected both rhizospheric and endospheric microbes (14).These studies have opened the way toward a new understanding of the composition and structure of plant microbiomes and the factors that affect them. However, this understanding is still at the initial stages, and several key questions are as yet unanswered. One such question regards the mechanism of microbiome acquisition and assembly in plants. Unlike animals, where the gut microbiome is assembled internally and is transmissible through birth (15, 16), the root microbiome is predominantly assembled from the external microbes in the soil. Based on the composition of the endospheric and rhizopheric microbiomes, it has been proposed that plants might assemble their microbiomes in two steps, with the first step involving a general recruitment to the vicinity of the root and a second step for entry inside the root that involves species-specific genetic factors (7). Although this is a plausible hypothesis, direct support for this model through detailed dynamic studies has not yet been provided. Additionally, the role of the root surface or rhizoplane, which forms the critical interface between plants and soil, remains poorly understood, and the microbial composition of the rhizoplane in relation to those of the rhizosphere and endosphere is unknown.To address some of these questions, we have undertaken an exhaustive characterization of the root-associated microbiome of rice. Rice is a major crop plant and a staple food for half of the world’s population. Metagenomic and proteomic approaches have been used to identify different microbial genes present in the rice microbiome (17, 18), but an extensive characterization of microbiome composition and variation has not been performed. Rice cultivation also contributes to global methane, accounting for an estimated 10–20% of anthropogenic emissions, due to the growth of methanogenic archaea in the vicinity of rice roots (19). Here we have used deep sequencing of microbial 16S rRNA genes to detect over 250,000 operational taxonomic units (OTUs), with a structural resolution of three distinct compartments (rhizosphere, rhizoplane, and endosphere) and extending over multiple factors contributing to variation, both under controlled greenhouse conditions as well as different field environments. The large datasets from the different conditions sampled in this study were used for identification of putative microbial consortia involved in processes such as methane cycling. Through dynamic studies of the microbiome composition, we provide insights into the process of root microbiome assembly.     

Oscillatory Behaviour of Ni Supported on ZrO2 in the Catalytic Partial Oxidation of Methane as Determined by Activation Procedure

Ni/ZrO₂ catalysts, active and selective for the catalytic partial oxidation of methane to syngas (CH₄-CPO), were prepared by the dry impregnation of zirconium oxyhydroxide (Z_hy) or monoclinic ZrO₂ (Z_m), calcination at 1173 K and activation by different procedures: oxidation-reduction (ox-red) or direct reduction (red). The characterization included XRD, FESEM, in situ FTIR and Raman spectroscopies, TPR, and specific surface area measurements. Catalytic activity experiments were carried out in a flow apparatus with a mixture of CH₄:O₂ = 2:1 in a short contact time. Compared to Z_m, Z_hy favoured the formation of smaller NiO particles, implying a higher number of Ni sites strongly interacting with the support. In all the activated Ni/ZrO₂ catalysts, the Ni–ZrO₂ interaction was strong enough to limit Ni aggregation during the catalytic runs. The catalytic activity depended on the activation procedures; the ox-red treatment yielded very active and stable catalysts, whereas the red treatment yielded catalysts with oscillating activity, ascribed to the formation of Ni^δ+ carbide-like species. The results suggested that Ni dispersion was not the main factor affecting the activity, and that active sites for CH₄-CPO could be Ni species at the boundary of the metal particles in a specific configuration and nuclearity.     

Additional Value of CH4 Measurement in a Combined 13C/H2 Lactose Malabsorption Breath Test: A Retrospective Analysis

The lactose hydrogen breath test is a commonly used, non-invasive method for the detection of lactose malabsorption and is based on an abnormal increase in breath hydrogen (H₂) excretion after an oral dose of lactose. We use a combined ¹³C/H₂ lactose breath test that measures breath ¹³CO₂ as a measure of lactose digestion in addition to H₂ and that has a better sensitivity and specificity than the standard test. The present retrospective study evaluated the results of 1051 ¹³C/H₂ lactose breath tests to assess the impact on the diagnostic accuracy of measuring breath CH₄ in addition to H₂ and ¹³CO₂. Based on the ¹³C/H₂ breath test, 314 patients were diagnosed with lactase deficiency, 138 with lactose malabsorption or small bowel bacterial overgrowth (SIBO), and 599 with normal lactose digestion. Additional measurement of CH₄ further improved the accuracy of the test as 16% subjects with normal lactose digestion and no H₂-excretion were found to excrete CH₄. These subjects should have been classified as subjects with lactose malabsorption or SIBO. In conclusion, measuring CH₄-concentrations has an added value to the ¹³C/H₂ breath test to identify methanogenic subjects with lactose malabsorption or SIBO.     

What happened: The chemistry side of the incident with EMS contamination in Viracept tablets

A technical review of the events leading to the global recall of Viracept film coated tablets 250 mg in June 2007 is given from the drug substance manufacturing perspective. Root cause analysis performed and corrective actions implemented are presented. Using the decay rate of ethyl methane sulfonate in Viracept film coated tablets 250 mg at 25 °C derived from stability studies, establishing of the worst case scenario for patient exposure to ethyl methane sulfonate, is outlined. Whereas the first evaluation based on ethyl methane sulfonate levels found in the drug substance suggested a worst case patient exposure of 2300 ppm, the decay rate of ethyl methane sulfonate in the drug product and the time gap between drug product manufacture and earliest possible use by patients led to the conclusion that 920 ppm (±10%) over a period of approx. 90 days is a reasonably cautious assumption for the worst case patient exposure scenario.     

Genotoxic evaluation of antiepileptic drugs by Drosophila somatic mutation and recombination test

The study examines the potential genotoxicity of three antiepileptic drugs (phenytoin sodium, pregabalin, gabapentin) using the wing somatic mutation and recombination test (SMART) in Drosophila melanogaster. Trans-heterozygous (two genetic markers mwh and flr) third-instar larvae of D. melanogaster were treated with different concentrations of the test compounds. A positive correlation was observed between total mutations and the number of wings with morphologically detectable mutations. The observed mutations were classified according to size and type of mutation per wing. Phenytoin clearly increased the frequency of total spots at all concentrations above 1.25 μg/ml. Gabapentin also increased the frequency of total spots at concentrations of 40 and 80 μg/ml. This study shows that phenytoin and gabapentin have genotoxic effects according to the SMART test; however, pregabalin displays lower genotoxicity in the SMAR assay when compared with the other two antiepileptics. The results also show that all AED concentrations lower the survival rate of the flies.     

孕期二苯基甲烷二异氰酸酯暴露对子代雄性小鼠性成熟后睾丸组织能量代谢功能的影响

目的探讨孕期二苯基甲烷二异氰酸酯(MDI)暴露对子代雄性小鼠性成熟后睾丸组织能量代谢功能的影响。方法将清洁级健康昆明种孕小鼠16只按体重随机分为高剂量(1/8LD50)、中剂量(1/16LD50)、低剂量(1/32LD50)MDI染毒组和溶剂对照组(玉米油),每组4只。于妊娠第14天开始,每日灌胃染毒,灌胃剂量为5ml/kg,持续至母鼠自然分娩。记录孕鼠染毒期间体重增量和分娩时间。待仔鼠8周龄(性成熟)时,分离双侧睾丸,称重,并计算睾丸的脏器系数。并检测睾丸组织中琥珀酸脱氢酶(SDH)、Na-K-ATP酶、Ca-Mg-ATP酶和总ATP酶的活力以及蛋白的含量。结果各组孕鼠分娩时间和体重增量间比较,差异均无统计学意义(P>0.05)。与高剂量MDI染毒组比较,中、低剂量MDI染毒组和溶剂对照组睾丸系数较高,差异均有统计学意义(P<0.01或P<0.05)。与溶剂对照组比较,高、中、低剂量MDI染毒组SDH、Na-K-ATPase、Ca-Mg-ATPase以及总ATPase酶活力均下降,差异均有统计学意义(P<0.01或P<0.05);且随着染毒剂量的增高,SDH、Na-K-ATPase、Ca-Mg-ATPase...     

Pathomorphological changes in rat brain choroid plexus due to administration of the amine-curing agent,bis(4-amino-3-methylcyclohexyl)methane

Summary Repeated oral administration of an amine-curing agent for epoxy resin, bis(4-amino-3-methylcyclohexyl)methane, gave rise to severe damage in the choroid plexus of rat brain. The damaged epithelium presented varying degrees of swelling and hydropic vacuolation on light microscopy, and varying numbers of vacuoles and inclusion bodies, frequently with lamellar structure, on transmission electron microscopy. Scanning electron microscopy of the choroid plexus disclosed some irregularity in the size of epithelial cells and occasional loss of microvilli. These changes in the choroid plexus were closely correlated with the dosage of the agent administered and the period of administration. In spite of the severe changes in the choroid plexus, no neurological abnormalities were observed in the animals during the experimental period.     

Catalysts Based on Strontium Titanate Doped with Ni/Co/Cu for Dry Reforming of Methane

Two series of strontium titanates doped with Ni, Co, or Cu with general formula of SrTi_1-xMe_xO₃ for Sr-stoichiometric and Sr_0.95Ti_1−xMe_xO₃ for Sr-non-stoichiometric materials (where Me = Ni, Co or Cu and x were 0.02 and 0.06) were obtained by the wet chemical method. The samples were calcinated at 900, 950, and 1050 °C and characterized in terms of their structural properties (XRD), the possibility of undergoing the reduction and oxidation reactions (TPR/TPOx), and catalytic properties. All obtained materials were multiphase and although the XRD analysis does not confirm the presence of Ni, Co, and Cu oxides (with one exception for Cu-doped sample), the TPR/TPOx profiles show reduction peaks that can be attributed to the reduction of these oxides which may at first appear in an amorphous form. Catalytic tests in dry reforming of methane reaction showed that the highest catalytic activity was achieved for Ni-doped materials (up to 90% of CH₄ conversion) while Co and Cu-doped samples showed only a very slight catalytic effect. Additionally, the decrease in methane conversion with an increasing calcination temperature was observed for Ni-doped strontium titanates.     

Anti-inflammatory and anti-arthritic activity of total flavonoids of the roots of Sophora flavescens

Ethnopharmacological relevance

The roots of Sophora flavescens have long been used in Chinese medicine for the treatment of fever, inflammatory disorders, ulcers and skin burns. Sophora flavescens contains flavonoids and alkaloids.

Aim of the study

This study was conducted to develop a plant-based anti-inflammatory agent focused on chronic inflammatory disorders. To accomplish this, the alkaloid-free prenylated flavonoid-enriched fraction (PFS) of rhizomes of Sophora flavescens was prepared and its in vitro and in vivo anti-inflammatory activities were then evaluated for the first time.

Materials and methods

The inhibitory activity of PFS on PGE₂, NO, IL-6 and TNF-α production of lipopolysaccharide (LPS)-treated RAW 264.7 cells was measured. Additionally, adjuvant-induced arthritis in rats was used as an animal model of chronic inflammation to establish the in vivo anti-inflammatory effects of PFS.

Result

PFS inhibited cyclooxygenase-2 (COX-2)-catalyzed PGE₂ and inducible nitric oxide synthase (iNOS)-catalyzed NO production by lipopolysaccharide (LPS)-treated RAW 264.7 cells at 10–50 μg/ml, and these effects primarily occurred via COX-2 inhibition and iNOS down-regulation, respectively. PFS also inhibited IL-6 and TNF-α production. When tested against adjuvant-induced arthritis in rats (chronic inflammation), PFS strongly inhibited arthritic inflammation when administered orally at doses of 10–100 mg/kg/day. In addition, PFS administered orally potently inhibited acetic acid-induced writhing in mice.

Conclusions

Our results suggest that PFS inhibits chronic inflammatory response and the inhibition of proinflammatory molecules such as COX-2, iNOS and IL-6 may contribute, at least in part, to the anti-inflammatory activity in vivo. Overall, these results indicate that PFS from Sophora flavescens may have the potential for treatment of chronic inflammatory disorders such as rheumatoid arthritis.