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

Bone Marrow Mesenchymal Cell Contribution in Maintenance of Periodontal Ligament Homeostasis

In general, remodeling phenomenon of the periodontal ligament (PDL) is occurring in all times. Thus, in the chapter, the word “maintenance” was used, and the chapter title is “Maintenance of Periodontal Ligament Homeostasis.” Our experimental data on the remodeling of the PDL with cell acceleration at the furcation area in this experimental model are recovered using the cells in situ and the bone marrow-derived cells (BMCs). BMC migration into the PDL tissues using green fluorescent protein (GFP) bone marrow-transplanted model mouse was examined. BMCs have abilities of cell migration and differentiation into tissues/organs in the body. The immunohistochemistry revealed that GFP-positive cells were detected in the PDL. GFP-positive cells were also positive to CD31, CD68, and Runx2 suggesting that fibroblasts differentiated into osteoclasts and tissue macrophages. In this way, Notch signaling involvement considered in our tentative examinations revealed that the experimentally induced periodontal polyp was examined; the cytological dynamics of the cells in granulation tissue are mainly from migration of undifferentiated mesenchymal cells of the bone marrow and differentiate into the tissue-specified cells. Furthermore, the data suggest that cell differentiation is due to Notch signaling

Minimal upstream open reading frame of Per2 mediates phase fitness of the circadian clock to day/night physiological body temperature rhythm

全身の体内リズムを調和させるRNA配列の発見 --体温の日内変化に合わせてしなやかに調和させる--. 京都大学プレスリリース. 2023-03-07.Body temperature in homeothermic animals does not remain constant but displays a regular circadian fluctuation within a physiological range (e.g., 35°C–38.5°C in mice), constituting a fundamental systemic signal to harmonize circadian clock-regulated physiology. Here, we find the minimal upstream open reading frame (uORF) encoded by the 5′ UTR of the mammalian core clock gene Per2 and reveal its role as a regulatory module for temperature-dependent circadian clock entrainment. A temperature shift within the physiological range does not affect transcription but instead increases translation of Per2 through its minimal uORF. Genetic ablation of the Per2 minimal uORF and inhibition of phosphoinositide-3-kinase, lying upstream of temperature-dependent Per2 protein synthesis, perturb the entrainment of cells to simulated body temperature cycles. At the organismal level, Per2 minimal uORF mutant skin shows delayed wound healing, indicating that uORF-mediated Per2 modulation is crucial for optimal tissue homeostasis. Combined with transcriptional regulation, Per2 minimal uORF-mediated translation may enhance the fitness of circadian physiology

Development and reliability of a standard rating system for outcome measurement of foot and ankle disorders I: development of standard rating system

AbstractBackgroundThe aim of this study was to report the five scales comprising the rating system that the Japanese Society for Surgery of the Foot (JSSF) devised (JSSF standard rating system) and the newly offered interpretations and criteria for determinations of each assessment item.MethodsWe produced the new scales for the JSSF standard system by modifying the clinical rating systems established by the American Orthopaedic Foot and Ankle Society (AOFAS scales) and the Japanese Orthopaedic Association’s foot rating scale (JOA scale). We also provided interpretations of each assessment item and the criteria of determinations in the new standard system.ResultsWe improved the ambiguous expressions and content in the conventional standard rating systems so they would be easily understood by Japanese people. The result was five scales in total. Four were designed for use specifically for ankle-hindfoot, midfoot, hallux metatarsophalangeal- interphalangeal, and lesser metatarsophalangeal- ineterphalangeal sites; and the fifth was for the foot and ankle with rheumatoid arthritis. Furthermore, we described interpretations and criteria for determinations with regard to evaluation items in each scale.ConclusionsConventionally, the AOFAS scales or the JOA scale have been separately applied depending on the sites or disorders concerned, but it was often difficult to decide on scores during practical evaluations because of differing expressions in different languages and also because of ambiguity in the interpretation of each evaluation item and in scoring standards as well. JSSF improved these scales and added definite interpretations of evaluation items as well as criteria for the rating (to be reported here in part I). Because these steps were expected to improve the reliability of outcomes assessed by each scale, we examined the reliability in scores of the newly developed scales, which are reported in part II (in this issue)

ABCC ゲンバク ショウガイ チョウサ イインカイ ブンショ オ ソザイ ニ シタ シリョウ ガゾウ デジタル アーカイビング モデル ノ サクセイ ニ カンスル ケンキュウ

研究報

Development and reliability of a standard rating system for outcome measurement of foot and ankle disorders II: interclinician and intraclinician reliability and validity of the newly established standard rating scales and Japanese Orthopaedic Association rating scale

AbstractBackgroundThis study evaluated the validity and inter- and intraclinician reliability of (1) the Japanese Society of Surgery of the Foot (JSSF) standard rating system for four sites [ankle- hindfoot (AH), midfoot (MF), hallux (HL), and lesser toe (LT)] and the rheumatoid arthritis (RA) foot and ankle scale and (2) the Japanese Orthopaedic Association’s foot rating scale (JOA scale).MethodsClinicians from the same institute independently evaluated participating patients from their institute by two evaluations at a 1- to 4-week interval. Statistical evaluation was as follows. (1) The intraclass correlation coefficient (ICC) was calculated from data collected from at least two examinations of each patient by at least two evaluating clinicians (Data A). (2) Total scores for the two evaluations were determined from the distribution of differences in data between the two evaluations (Data B); each item was evaluated by determining Cohen’s coefficient of agreement. (3) The relation between patient satisfaction and total score was investigated only for patients who underwent surgery (Data C). Spearman’s rank correlation coefficient was obtained.ResultsParticipants were 65 clinicians and 610 patients, including those with disorders of the AH (313), MF (47), HL (153), and LT (50) and those with RA (47). From Data A, the ICC was high for AH and HL by JSSF scales and for AH, MF, and LT by the JOA scale. From Data B, the coefficient showed high validity for both scales for AH, with almost no difference between the two scales; the validity for HL was higher with the JOA scale than with the JSSF scale. From Data C, correlations were significant between patient satisfaction and outcome for AH and HL by the JSSF scales and for AH, HL, and LT by the JOA scale.ConclusionsThe validity of both scales was high. Clinical evaluation of the therapeutic results using these scales would be highly reliable

Chapter 6 : Bone marrow masenchymal cell contribution in maintenance of periodontal ligament homeostasis.

In general, remodeling phenomenon of the periodontal ligament (PDL) is occurring in all times. Thus, in the chapter, the word “maintenance” was used, and the chapter title is “Maintenance of Periodontal Ligament Homeostasis.” Our experimental data on the remodeling of the PDL with cell acceleration at the furcation area in this experimental model are recovered using the cells in situ and the bone marrow-derived cells (BMCs).BMC migration into the PDL tissues using green Ěuorescent protein (GFP)bone　marrow-transplanted model mouse was examined. BMCs have abilities of　cell migration and diěerentiation into　tissues/organs in the body. The immunohistochemistry revealed that GFP-positive cells were detected in the PDL.GFP-positive cells were also positive to CD31, CD68, and Runx2 suggesting that ębroblasts diěerentiated into osteoclasts and tissue macrophages. In this　way, Notch signaling involvement considered in our tentative examinations revealed　that the experimentally induced periodontal polyp was examined; the cytological　dynamics of the cells in granulation tissue are mainly from migration of　undiěerentiated mesenchymal cells of the bone marrow and diěerentiate into the　tissue-specięed cells. Furthermore, the data suggest that cell diěerentiation is due to　Notch signaling.Edited by Thomas Heinbockel and Vonnie D.C. Shields : Published in London : IntechOpen, 2019

Predictive Factors of the Fatality of Motor Vehicle Passengers Involved in Far-Side Lateral Collisions: A National Crash Database Study

Although the risks faced by passengers in near-side lateral collisions are understood, and despite the presence of side airbags for injury prevention, passengers involved in far-side lateral collisions also suffer serious and fatal injuries. The objective of this study was to determine the independent predictive factors of fatality of motor vehicle passengers involved in far-side lateral collisions. Using 2010 records from the National Automotive Sampling System/Crashworthiness Data System (NASS/CDS), we selected 86 fatal and 325 non-fatal passengers with an Abbreviated Injury Scale (AIS) score of 2 or more. The background and injury severity of the passengers and collision characteristics were compared between the two groups. In a multivariable logistic regression analysis, variables independently associated with fatalities were female sex (Ref, male) (odds ratio [OR], 0.396), age (OR, 1.029), body mass index (OR, 1.057), total delta-V (OR, 1.031), head AIS score (OR, 1.679), chest AIS score (OR, 1.330), and abdomen AIS score (OR, 1.294). This is the first report to determine factors affecting fatality in passengers involved in far-side lateral collisions. Improving the safety of the vehicle interior, such as by including additional seatbelt systems or a side airbag that deploys between seats, might help to avoid fatalities, and reduce injury severity