Massively parallel single-cell genomics of microbiomes in rice paddies

世界初のイネ根圏微生物叢の網羅的1細胞ゲノム解析に成功 --コメ生産現場が抱える問題のデータベース化に向けて--. 京都大学プレスリリース. 2022-11-09.Plant growth-promoting microbes (PGPMs) have attracted increasing attention because they may be useful in increasing crop yield in a low-input and sustainable manner to ensure food security. Previous studies have attempted to understand the principles underlying the rhizosphere ecology and interactions between plants and PGPMs using ribosomal RNA sequencing, metagenomic sequencing, and genome-resolved metagenomics; however, these approaches do not provide comprehensive genomic information for individual species and do not facilitate detailed analyses of plant–microbe interactions. In the present study, we developed a pipeline to analyze the genomic diversity of the rice rhizosphere microbiome at single-cell resolution. We isolated microbial cells from paddy soil and determined their genomic sequences by using massively parallel whole-genome amplification in microfluidic-generated gel capsules. We successfully obtained 3, 237 single-amplified genomes in a single experiment, and these genomic sequences provided insights into microbial functions in the paddy ecosystem. Our approach offers a promising platform for gaining novel insights into the roles of microbes in the rice rhizomicrobiome and to develop microbial technologies for improved and sustainable rice production

Sucrose starvation induces microautophagy in plant root cells

Abstract Autophagy is an essential system for degrading and recycling cellular components for survival during starvation conditions. Under sucrose starvation, application of a papain protease inhibitor E-64d to the Arabidopsis root and tobacco BY-2 cells induced the accumulation of vesicles, labeled with a fluorescent membrane marker FM4-64. The E-64d-induced vesicle accumulation was reduced in the mutant defective in autophagy-related genes ATG2, ATG5, and ATG7, suggesting autophagy is involved in the formation of these vesicles. To clarify the formation of these vesicles in detail, we monitored time-dependent changes of tonoplast, and vesicle accumulation in sucrose-starved cells. We found that these vesicles were derived from the tonoplast and produced by microautophagic process. The tonoplast proteins were excluded from the vesicles, suggesting that the vesicles are generated from specific membrane domains. Concanamycin A treatment in GFP-ATG8a transgenic plants showed that not all FM4-64-labeled vesicles, which were derived from the tonoplast, contained the ATG8a-containing structure. These results suggest that ATG8a may not always be necessary for microautophagy.This study was supported by the National Science Centre, Poland [UMO-2016/21/P/NZ9/01089 to SG-Y (the project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 665778) and UMO-2016/23/B/NZ1/01847 to KeY]; the Foundation for Polish Science (TEAM/2017-4/41 to KeY); KAKENHI from the Japan Society for the Promotion of Science, Japan (JP15J40032 to SG-Y, JP17K07457 to SM, and JP15H05776 to IH-N); and KAKENHI from the Ministry of Education, Culture, Sports, Science and Technology, Japan (JP26111523 to SG-Y); as well as the institutional support provided from the National Institute for Basic Biology (NIBB), Kyoto University, and Małopolska Centre of Biotechnology, Jagiellonian University. Next-generation sequencing was supported by NIBB Collaborative Research Programs 11-711

Pexophagy suppresses ROS-induced damage in leaf cells under high-intensity light

Although light is essential for photosynthesis, it has the potential to elevate intracellular levels of reactive oxygen species (ROS). Since high ROS levels are cytotoxic, plants must alleviate such damage. However, the cellular mechanism underlying ROS-induced leaf damage alleviation in peroxisomes was not fully explored. Here, we show that autophagy plays a pivotal role in the selective removal of ROS-generating peroxisomes, which protects plants from oxidative damage during photosynthesis. We present evidence that autophagy-deficient mutants show light intensity-dependent leaf damage and excess aggregation of ROS-accumulating peroxisomes. The peroxisome aggregates are specifically engulfed by pre-autophagosomal structures and vacuolar membranes in both leaf cells and isolated vacuoles, but they are not degraded in mutants. ATG18a-GFP and GFP-2×FYVE, which bind to phosphatidylinositol 3-phosphate, preferentially target the peroxisomal membranes and pre-autophagosomal structures near peroxisomes in ROS-accumulating cells under high-intensity light. Our findings provide deeper insights into the plant stress response caused by light irradiation

Antenatal antiarrhythmic treatment for fetal tachyarrhythmias: a study protocol for a prospective multicentre trial

Introduction Several retrospective or single-centrestudies demonstrated the efficacy of transplacentaltreatment of fetal tachyarrhythmias. Our retrospectivenationwide survey showed that the fetal therapy willbe successful at an overall rate of 90%. For fetuseswith hydrops, the treatment success rate will be 80%.However, standard protocol has not been established.The objective of this study is to evaluate the efficacy andsafety of the protocol-defined transplacental treatment offetal tachyarrhythmias. Participant recruitment began inOctober 2010.Methods and analysis The current study is a multicentre,single-arm interventional study. A total of 50 fetuseswill be enrolled from 15 Japanese institutions. Theprotocol-defined transplacental treatment is performed forsingletons with sustained fetal tachyarrhythmia ≥180 bpm,with a diagnosis of supraventricular tachycardia or atrialflutter. Digoxin, sotalol, flecainide or a combination is usedfor transplacental treatment. The primary endpoint isdisappearance of fetal tachyarrhythmias. The secondaryendpoints are fetal death related to tachyarrhythmia,proportion of preterm birth, rate of caesarean sectionattributable to fetal arrhythmia, improvement in fetalhydrops, neonatal arrhythmia, neonatal central nervoussystem disorders and neonatal survival. Maternal, fetal andneonatal adverse events are evaluated at 1 month afterbirth. Growth and development are also evaluated at 18and 36 months of corrected age.Ethics and dissemination The Institutional Review Boardof the National Cerebral and Cardiovascular Center ofJapan has approved this study. Our findings will be widelydisseminated through conference presentations and peerreviewedpublications

Low-Dose Intravenous Alteplase in Wake-Up Stroke

Background and Purpose—We assessed whether lower-dose alteplase at 0.6 mg/kg is efficacious and safe for acute fluid-attenuated inversion recovery-negative stroke with unknown time of onset. Methods—This was an investigator-initiated, multicenter, randomized, open-label, blinded-end point trial. Patients met the standard indication criteria for intravenous thrombolysis other than a time last-known-well >4.5 hours (eg, wake-up stroke). Patients were randomly assigned (1:1) to receive alteplase at 0.6 mg/kg or standard medical treatment if magnetic resonance imaging showed acute ischemic lesion on diffusion-weighted imaging and no marked corresponding hyperintensity on fluid-attenuated inversion recovery. The primary outcome was a favorable outcome (90-day modified Rankin Scale score of 0–1). Results—Following the early stop and positive results of the WAKE-UP trial (Efficacy and Safety of MRI-Based Thrombolysis in Wake-Up Stroke), this trial was prematurely terminated with 131 of the anticipated 300 patients (55 women; mean age, 74.4±12.2 years). Favorable outcome was comparable between the alteplase group (32/68, 47.1%) and the control group (28/58, 48.3%; relative risk [RR], 0.97 [95% CI, 0.68–1.41]; P=0.892). Symptomatic intracranial hemorrhage within 22 to 36 hours occurred in 1/71 and 0/60 (RR, infinity [95% CI, 0.06 to infinity]; P>0.999), respectively. Death at 90 days occurred in 2/71 and 2/60 (RR, 0.85 [95% CI, 0.06–12.58]; P>0.999), respectively. Conclusions—No difference in favorable outcome was seen between alteplase and control groups among patients with ischemic stroke with unknown time of onset. The safety of alteplase at 0.6 mg/kg was comparable to that of standard treatment. Early study termination precludes any definitive conclusions

Functions of plant-specific myosin XI: from intracellular motility to plant postures.

Available online 30 September 2015The plant-specific protein motor class myosin XI is known to function in rapid bulk flow of the cytoplasm (cytoplasmic streaming) and in organellar movements. Recent studies unveiled a wide range of physiological functions of myosin XI motors, from intracellular motility to organ movements. Arabidopsis thaliana has 13 members of myosin XI class. In vegetative organs, myosins XIk, XI1, and XI2 primarily contribute to dynamics and spatial configurations of endoplasmic reticulum that develops a tubular network in the cell periphery and thick strand-like structures in the inner cell regions. Myosin XI-i forms a nucleocytoplasmic linker and is responsible for nuclear movement and shape. In addition to these intracellular functions, myosin XIf together with myosin XIk is involved in the fundamental nature of plants; the actin-myosin XI cytoskeleton regulates organ straightening to adjust plant posture

Leguminous wood has a unique vacuolar lectin in bark : Lectin-carbohydrate interaction modulates solubility-insolubility transition of vacuolar glycoproteins

Mannose/glucose-specific sophoragrin, a Sophora japonica bark lectin, shows unique multimerization and dissociation accompanied by transitions between insolubility and solubility, which are modulated by both a specific sugar and Ca^<2+> concentration. Sophoragrin is composed of four subunits, a-1, a-2, b-1, and b-2, and all except for b-2 are reported to be glycosylated. Biotinylated sophoragrin bound sugar-specifically to subunit 'b' but not to subunit 'a' on the membrane. Sophoragrin was labeled by only one of the photoaffinity-probes derived from sophoragrin-glycans, and the labeling was inhibited by a specific sugar. In contrast, another probe-mixture, which contains major oligosaccharide of sophoragrin (Man_3Xyl_1Fuc_1GlcNAc_2), did not label sophoragrin. These results reveal that the multimerization of sophoragrin is caused by a particular signal oligosaccharide on subunit 'b'. It was shown that sophoragrin can form a soluble complex with other endogenous glycoproteins, and may play a specific role through its transition between soluble and insoluble forms

Survivability from a Managerial Economic Perspective: Dairy Farming and Rice Farming in Japan

Special Issue: Works from "Future Leaders Global Workshop on Social Science of Agriculture, Food and Environment"Over the past few years, Japanese agricultural holdings have been facing challenging conditions in terms of fluctuating food demand as well as a decline in food prices. This paper clarifies managerial survivability from two standpoints: temporary and permanent, applying two analytical methods. First, we employ ‘Expense-income analysis' to investigate temporary managerial survivability (TMS), which is realised when an agricultural holding's gross income is above or equal to operating expense. Second, we employ Minimum Required Operating Scale (MROS) analysis to investigate permanent managerial survivability (PMS), which is realised when a holding can afford one additional unit of the scarcest resource. We analyse the dairy and rice farming sectors in Japan. Our findings reveal that it is not only imperative for holdings to enlarge their farming scale, but also to more essentially take into account improvements in managerial environments