Wild species rice OsCERK1DY-mediated arbuscular mycorrhiza symbiosis boosts yield and nutrient use efficiency in rice breeding.

Meeting the ever-increasing food demands of a growing global population while ensuring resource and environmental sustainability presents significant challenges for agriculture worldwide. Arbuscular mycorrhizal symbiosis (AMS) has emerged as a potential solution by increasing the surface area of a plant's root system and enhancing the absorption of phosphorus, nitrogen nutrients, and water. Consequently, there is a longstanding hypothesis that rice varieties exhibiting more efficient AMS could yield higher outputs at reduced input costs, paving the way for the development of Green Super Rice (GSR). Our prior research study identified a variant, OsCERK1DY, derived from Dongxiang wild-type rice, which notably enhanced AMS efficiency in the rice cultivar "ZZ35." This variant represents a promising gene for enhancing yield and nutrient use efficiency in rice breeding. In this study, we conducted a comparative analysis of biomass, crop growth characteristics, yield attributes, and nutrient absorption at varying soil nitrogen levels in the rice cultivar "ZZ35" and its chromosome single-segment substitution line, "GJDN1." In the field, GJDN1 exhibited a higher AM colonization level in its roots compared with ZZ35. Notably, GJDN1 displayed significantly higher effective panicle numbers and seed-setting rates than ZZ35. Moreover, the yield of GJDN1 with 75% nitrogen was 14.27% greater than the maximum yield achieved using ZZ35. At equivalent nitrogen levels, GJDN1 consistently outperformed ZZ35 in chlorophyll (Chl) content, dry matter accumulation, major nutrient element accumulation, N agronomic efficiency (NAE), N recovery efficiency (NRE), and N partial factor productivity (NPFP). The performance of OsCERK1DY overexpression lines corroborated these findings. These results support a model wherein the heightened level of AMS mediated by OsCERK1DY contributes to increased nitrogen, phosphorus, and potassium accumulation. This enhancement in nutrient utilization promotes higher fertilizer efficiency, dry matter accumulation, and ultimately, rice yield. Consequently, the OsCERK1DY gene emerges as a robust candidate for improving yield, reducing fertilizer usage, and facilitating a transition towards greener, lower-carbon agriculture. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01459-8.

Epigenome-wide methylation haplotype association analysis identified HLA-DRB1, HLA-DRB5 and HLA-DQB1 as risk factors for rheumatoid arthritis.

The aim of this study was to compare nonrandom associations between physically adjacent single methylation polymorphism loci among rheumatoid arthritis (RA) and normal subjects for investigating RA-risk methylation haplotypes (meplotype). With 354 ACPA-positive RA patients and 335 normal controls selected from a case-control study based on Swedish population, we conducted the first RA epigenome-wide meplotype association study using our software EWAS2.0, mainly including (i) converted the ß value to methylation genotype (menotype) data, (ii) identified methylation disequilibrium (MD) block, (iii) calculated frequent of each meplotypes in MD block and performed case-control association test and (iv) screened for RA-risk meplotypes by odd ratio (OR) and p-values. Ultimately, 545 meplotypes on 334 MD blocks were identified significantly associated with RA (p-value < .05). These meplotypes were mapped to 329 candidate genes related to RA. Subsequently, combined with gene optimization, eight RA-risk meplotypes were identified on three risk genes: HLA-DRB1, HLA-DRB5 and HLA-DQB1. Our results reported the relationship between DNA methylation pattern on HLA-DQB1 and the risk of RA for the first time, demonstrating the co-demethylation of 'cg22984282' and 'cg13423887' on HLA-DQB1 gene (meplotype UU, p-value = 2.90E - 6, OR = 1.68, 95% CI = [1.35, 2.10]) may increase the risk of RA. Our results demonstrates the potential of methylation haplotype analysis to identify RA-related genes from a new perspective and its applicability to the study of other disease.

[Research on Management Efficiency of Hospital Low-value Consumables in Nursing Unit under Lean Management Mode].

Aiming at the management efficiency problems in the traditional medical low-value consumables management mode of the nursing unit, based on the perspective of supply chain management, this study uses lean management method to construct the lean management mode of low-value consumables with a whole cycle and whole process information monitoring, and analyzes the application effect of this mode. The results show that after the application of lean management mode, the low-value consumables of the nursing unit can achieve "consumables in use=priced consumables + un-priced consumables", the settlement cost is significantly reduced and its stability is high, and the efficiency of "supply-inventor-distribution" link is significantly enhanced. This model effectively improves the management efficiency of low-value consumables in the hospital, and also provides a reference for other hospitals to improve the management level of low-value consumables.

Integrated 16S and metabolomics revealed the mechanism of drought resistance and nitrogen uptake in rice at the heading stage under different nitrogen levels.

The normal methods of agricultural production worldwide have been strongly affected by the frequent occurrence of drought. Rice rhizosphere microorganisms have been significantly affected by drought stress. To provide a hypothetical basis for improving the drought resistance and N utilization efficiency of rice, the study adopted a barrel planting method at the heading stage, treating rice with no drought or drought stress and three different nitrogen (N) levels. Untargeted metabolomics and 16S rRNA gene sequencing technology were used to study the changes in microorganisms in roots and the differential metabolites (DMs) in rhizosphere soil. The results showed that under the same N application rate, the dry matter mass, N content and N accumulation in rice plants increased to different degrees under drought stress. The root soluble protein, nitrate reductase and soil urease activities were improved over those of the no-drought treatment. Proteobacteria, Bacteroidota, Nitrospirota and Zixibacteria were the dominant flora related to N absorption. A total of 184 DMs (98 upregulated and 86 downregulated) were identified between low N with no drought (LN) and normal N with no drought (NN); 139 DMs (83 upregulated and 56 downregulated) were identified between high N with no drought (HN) and NN; 166 DMs (103 upregulated and 63 downregulated) were identified between low N with drought stress (LND) and normal N with drought stress (NND); and 124 DMs (71 upregulated and 53 downregulated) were identified between high N with drought stress (HND) and NND. Fatty acyl was the metabolite with the highest proportion. KEGG analysis showed that energy metabolism pathways, such as D-alanine metabolism and the phosphotransferase system (PTS), were enriched. We conclude that N-metabolism enzymes with higher activity and higher bacterial diversity have a significant effect on drought tolerance and nitrogen uptake in rice.

RABC: Rheumatoid Arthritis Bioinformatics Center.

Advances in sequencing technologies have led to the rapid growth of multi-omics data on rheumatoid arthritis (RA). However, a comprehensive database that systematically collects and classifies the scattered data is still lacking. Here, we developed the Rheumatoid Arthritis Bioinformatics Center (RABC, http://www.onethird-lab.com/RABC/), the first multi-omics data resource platform (data hub) for RA. There are four categories of data in RABC: (i) 175 multi-omics sample sets covering transcriptome, epigenome, genome, and proteome; (ii) 175 209 differentially expressed genes (DEGs), 105 differentially expressed microRNAs (DEMs), 18 464 differentially DNA methylated (DNAm) genes, 1 764 KEGG pathways, 30 488 GO terms, 74 334 SNPs, 242 779 eQTLs, 105 m6A-SNPs and 18 491 669 meta-mQTLs; (iii) prior knowledge on seven types of RA molecular markers from nine public and credible databases; (iv) 127 073 literature information from PubMed (from 1972 to March 2022). RABC provides a user-friendly interface for browsing, searching and downloading these data. In addition, a visualization module also supports users to generate graphs of analysis results by inputting personalized parameters. We believe that RABC will become a valuable resource and make a significant contribution to the study of RA.

Identification of novel meQTLs strongly associated with rheumatoid arthritis by large-scale epigenome-wide analysis.

Rheumatoid arthritis (RA) is highly heritable, and previous studies have suggested that genetic variation may affect susceptibility to RA by altering epigenetic modifications (e.g. DNA methylation). Here we examined how genetic variation influences DNA methylation (DNAm) in RA by integrating individual genetic variation and DNAm data. Epigenome-wide meQTL (methylation quantitative trait loci) analysis was performed on 354 RA patients and 335 controls, scanning 30,101,744 relationships between 62 SNPs and 485,512 DNA methylation sites. Two regulatory relationship pairs (FDR < 0.05) showed very strong associations with RA risk. One was rs10796216-cg00475509, and the DNAm decreased by 0.0168 per addition of allele rs10796216-A. The other was rs6546473-cg13358873, for which a 0.0365 reduction of DNAm at cg13358873 was observed for each addition of allele rs6546473-A, and lower DNAm was found to be significantly associated with RA risk (P = 2.0407e-28). Moreover, both pairs of meQTL showed a strong regulatory relationship only in RA samples, so they can be subsequently considered as risk markers for RA. In conclusion, our integrated analysis of genetic and epigenetic variation suggests that genetic variation may affect the risk of RA by regulating DNA methylation levels. Alterations of DNAm at cg00475509 and cg13358873 loci conferred by rs10796216-A and rs6546473-A allele may suggest a potential risk for RA. Our results deepen our understanding of the genetic and epigenetic mechanisms of RA and provide novel associations that can be further investigated in future studies.

Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.).

Heterosis is a common biological phenomenon that is useful for breeding superior lines. Using heterosis to increase the yield and quality of crops is one of the main achievements of modern agricultural science. In this study, we analysed the transcriptome and metabolome of two three-line hybrid rice varieties, Taiyou 871 (TY871), and Taiyou 398 (TY398) and the parental grain endosperm using RNA-seq (three biological repeats per variety) and untargeted metabolomic (six biological repeats per variety) methods. TY871 and TY398 showed specific heterosis in yield and quality. Transcriptome analysis of the hybrids revealed 638 to 4059 differentially expressed genes in the grain when compared to the parents. Metabolome analysis of the hybrids revealed 657 to 3714 differential grain metabolites when compared to the parents. The honeydew1 and grey60 module core genes Os04g0350700 and Os05g0154700 are involved in the regulation of awn development, grain size, and grain number, as well as the regulation of grain length and plant height, respectively. Rice grain length may be an important indicator for improving the quality of three-line hybrid rice. In addition, the rice quality-related metabolite NEG_M341T662 was highly connected to the module core genes Os06g0254300 and Os03g0168100. The functions of Os06g0254300 and Os03g0168100 are EF-hand calcium binding protein and late embroideries absolute protein repeat containing protein, respectively. These genes may play a role in the formation of rice quality. We constructed a gene and metabolite coexpression network, which provides a scientific basis for the utilization of heterosis in producing high-yield and high-quality hybrid rice.

Mobile-Based and Self-Service Tool (iPed) to Collect, Manage, and Visualize Pedigree Data: Development Study.

BACKGROUND: Pedigree data (family history) are indispensable for genetics studies and the assessment of individuals' disease susceptibility. With the popularity of genetics testing, the collection of pedigree data is becoming more common. However, it can be time-consuming, laborious, and tedious for clinicians to investigate all pedigree data for each patient. A self-service robot could inquire about patients' family history in place of professional clinicians or genetic counselors. OBJECTIVE: The aim of this study was to develop a mobile-based and self-service tool to collect and visualize pedigree data, not only for professionals but also for those who know little about genetics. METHODS: There are 4 main aspects in the iPed construction, including interface building, data processing, data storage, and data visualization. The user interface was built using HTML, JavaScript libraries, and Cascading Style Sheets (version 3; Daniel Eden). Processing of the submitted data is carried out by PHP programming language. MySQL is used to document and manage the pedigree data. PHP calls the R script to accomplish the visualization. RESULTS: iPed is freely available to all users through the iPed website. No software is required to be installed, no pedigree files need to be prepared, and no knowledge of genetics or programs is required. The users can easily complete their pedigree data collection and visualization on their own and through a dialogue with iPed. Meanwhile, iPed provides a database that stores all users' information. Therefore, when the users need to construct new pedigree trees for other genetic traits or modify the pedigree trees that have already been created, unnecessary duplication of operations can be avoided. CONCLUSIONS: iPed is a mobile-based and self-service tool that could be used by both professionals and nonprofessionals at any time and from any place. It reduces the amount of time required to collect, manage, and visualize pedigree data.

[Practice of Refined Management of in Vitro Diagnostic Reagents Based on SPD in Hospital].

The management of in vitro diagnostic reagents has always been a concern. This paper describes the application of SPD medical consumables fine management system in our hospital. Relying on the brand-new management mode, the whole process from supplier qualification certificate management, in vitro diagnostic reagent procurement management, secondary warehouse management, and then to the use process traceability was realized. The monthly cost of in vitro diagnostic reagents can be accurately counted, which effectively controls the cost of in vitro diagnostic reagents.

The regular pattern and underlying mechanisms of seawater intrusion in the Modaomen channel in the Pearl River Estuary of China.

In recent decades, the frequency and severity of inland river seawater intrusion has increased in the Pearl River Estuary (PRE) of China. Based on time series of water salinity data, river discharges, tides, and wind records for the period 2003-2015, this study aims to examine the regular pattern and underlying mechanisms of the seawater intrusion in the Modaomen channel of the PRE. Toward this end, the autocorrelation and spectral analysis are used to quantify the periodicity of runoff, tide, and water salinity and to infer the regular patterns of seawater intrusion. The Pearson correlation and the LMG metric are used to examine the effects of influencing factors on seawater intrusion. Results indicate that seawater intrusion in the Modaomen channel has distinct annual (369 days) and half-monthly (14.8 days) cycles, corresponding well with annual and half-monthly tidal cycles. Spatially, the frequency, severity, and periodicity of seawater intrusion decrease with increased landward distance away from the channel mouth. The prevention of seawater intrusion by incoming river flow becomes more remarkable as freshwater flows downstream. Shifts in wind speed and direction can strengthen or weaken seawater intrusion, depending on if wind is in the opposite or same direction of river flow. Further analysis using the LMG metric suggests that river discharge plays a dominant role in governing seawater intrusion. Overall, river discharges, tides, and wind are three major forces triggering the inland river seawater intrusion and account for, respectively, 46%, 15%, and 15% of the variation of water salinity in the Modaomen channel. The study is featured in not only identifying the major factors in driving seawater intrusion but also quantifying their relative contribution. Thus, the findings are important for water resources manager to predict and manage inland river seawater intrusion in the PRE of China.

Unraveling the relative impacts of climate change and human activities on grassland productivity in Central Asia over last three decades.

Climate change (CC) and human activities (HA) have severely influenced grassland productivity in Central Asia since the 1980s. However, the relative impacts of CC and HA on grassland productivity are not adequately documented, especially over the past three decades. In this study, we adapted the Ensemble Empirical Mode Decomposition (EEMD) to reveal potential timescales at which grassland productivity varied in Central Asia and to investigate the spatiotemporal variations of grassland productivity during 1982-2015. We developed a quantitative method that incorporated the EEMD, along with six scenarios, to disentangle the effects of CC and HA on grassland productivity in Central Asia. Results showed that grassland productivity in Central Asia trended upward significantly at a rate of 0.66 gC m-2 yr-1 and was dominated by a 3-year time scale oscillation. The impacts of CC and HA on grassland productivity varied significantly over space and time. CC mainly facilitated grassland productivity restoration, whereas HA decreased grassland productivity in Central Asia. Besides, varied HA in six regions of Central Asia were due to different policy implementations across these regions. In particular, HA in Xinjiang significantly promoted grassland restoration, accounting for 22.5% of the total human-affected area, mostly because of the implementation of the Grazing Withdrawal Program (GWP), while HA significantly accelerated grassland productivity degradation in Uzbekistan and Turkmenistan over last three decades. Additionally, HA promoted the restoration of grassland productivity in Kazakhstan in a short period due to the disintegration of the Soviet Union, but degraded it at long-term scale. Further, precipitation was found to be the main climatic factor while grazing be the main human factor for controlling grassland productivity variations in Central Asia, respectively. Overall, our study provides not only a novel way of quantifying the impacts of CC and HA on vegetation variations but also new insights into mechanisms mediating grassland productivity in Central Asia.

[Construction of Quality Control System for Medical Equipment under the Model of County Medical Service Community].

The construction of county and district medical community is an important measure for high-quality medical resources to "double sink and improve". In this study, we have initially constructed a medical equipment quality control system for members of the regional medical community. The current situation of lack of professional medical equipment management personnel and quality control equipment in primary medical institutions has been alleviated, the quality control level of medical equipment in primary medical institutions has been improved, and a new management model for quality control of primary medical equipment has been explored.

EWASdb: epigenome-wide association study database.

DNA methylation, the most intensively studied epigenetic modification, plays an important role in understanding the molecular basis of diseases. Furthermore, epigenome-wide association study (EWAS) provides a systematic approach to identify epigenetic variants underlying common diseases/phenotypes. However, there is no comprehensive database to archive the results of EWASs. To fill this gap, we developed the EWASdb, which is a part of 'The EWAS Project', to store the epigenetic association results of DNA methylation from EWASs. In its current version (v 1.0, up to July 2018), the EWASdb has curated 1319 EWASs associated with 302 diseases/phenotypes. There are three types of EWAS results curated in this database: (i) EWAS for single marker; (ii) EWAS for KEGG pathway and (iii) EWAS for GO (Gene Ontology) category. As the first comprehensive EWAS database, EWASdb has been searched or downloaded by researchers from 43 countries to date. We believe that EWASdb will become a valuable resource and significantly contribute to the epigenetic research of diseases/phenotypes and have potential clinical applications. EWASdb is freely available at http://www.ewas.org.cn/ewasdb or http://www.bioapp.org/ewasdb.

The variation of vegetation greenness and underlying mechanisms in Guangdong province of China during 2001-2013 based on MODIS data.

This study explored the spatiotemporal variation of vegetation greenness and the mechanisms underlying this variation in the subtropical region of Guangdong in China during 2001-2013 to obtain a better understanding of vegetation response to climate and land use/cover changes in warm-humid regions. Satellite-based vegetation indices, land use/cover data and observed weather records during 2001-2013 were used. Univariate and multivariate linear regressions were conducted to quantify the trends and variations in vegetation greenness and the relationships with climate and land use/cover changes. The results indicated that the annual mean greenness trended upward significantly in eastern and western Guangdong and downward significantly in northern Guangdong. The patterns of significant positive or negative relationships between vegetation greenness and climatic factors were observed at the sub-regional scale. In addition, our results showed that (i) vegetation greenness in Guangdong was more sensitive to changes in temperature than in precipitation, (ii) spring temperature had an important time-lag effect on seasonal mean greenness in the following summer and autumn, and (iii) winter greenness depended largely on vegetation growth in the previous autumn. Furthermore, the conversion of grasslands and croplands to evergreen forests resulting from afforestation increased the vegetation greenness in eastern and western Guangdong. Overall, our results suggest that afforestation plays a dominant role in increasing vegetation cover/greenness in Guangdong whereas the effects of land use/cover change on vegetation growth are subject to climatic conditions. Thus, a better understanding of terrestrial vegetation dynamics requires considering both climate and land use/cover changes.

Response to Nitrogen Deficiency and Compensation on Physiological Characteristics, Yield Formation, and Nitrogen Utilization of Rice.

Based on the theory of ecological crop nutrient deficiency and compensation effect, the nitrogen (N) deficiency at tillering stage and N compensation at young panicle differentiation stage in rice (Oryza sativa L.) was selected to study. Four N treatments were treated, and the effects of N deficiency and compensation were investigated on grain yield, N uptake and utilization and the physiological characteristics of rice. The results showed that the yield per plant presented an equivalent compensatory effect. Double N compensation led to superiority in the number of effective panicle per plant, increased the activity of nitrate reductase and glutamine synthetase. The content of endogenous growth-inhibitory hormone abscisic acid (ABA) decreased in the leaves, photosynthesis was enhanced, and the number of tillers per plant increased after double N compensation. During maturation stage, the panicle dry weigh in T1 (double N compensation at young panicle differentiation stage, after N deficiency at tillering stage) was higher than that in CK1 (constant supply of N throughout different stages of growth) and the biomass per plant in T1 increased by 1.47% compared with CK1. N contents in all organs, N accumulation, and total N content were all higher in T1 during maturation stage. Moreover, N agronomic efficiency, N physiological efficiency, and N partial factor productivity were optimized for T1 and CK2 (constant N compensation at young panicle differentiation stage, after N deficiency at tillering stage) compared with CK1. This study contributes to the understanding of the physiological mechanisms underlying the compensation of N deficiency in rice.

A Comparison of Co-methylation Relationships Between Rheumatoid Arthritis and Parkinson's Disease.

Rheumatoid arthritis (RA) is a complex autoimmune disease. Recent studies have identified the DNA methylation loci associated with RA and found that DNA methylation was a potential mediator of genetic risk. Parkinson's disease (PD) is a common neurodegenerative disease. Several studies have indicated that DNA methylation levels are linked to PD, and genes related to the immune system are significantly enriched in PD-related methylation modules. Although recent studies have provided profound insights into the DNA methylation of both RA and PD, no shared co-methylation relationships have been identified to date. Therefore, we sought to identify shared co-methylation relationships linked to RA and PD. Here, we calculated the Pearson's correlation coefficient (PCC) of 225,239,700 gene pairs and determined the differences and similarities between the two diseases. The global co-methylation change between in PD cases and controls was larger than that between RA cases and controls. We found 337 gene pairs with large changes that were shared between RA and PD. This co-methylation relationship study represents a new area of study for both RA and PD and provides new ideas for further study of the shared biological mechanisms of RA and PD.

[The Traceability Management for Qualification Documents of Medical Instruments].

The management for qualification documents of medical instruments is very important work to management department of medical instruments. Because the number of qualification documents of medical instruments is very large and they have an expiry date, it is difficult to manage them. This article discussed how to manage qualification documents of medical instruments, and an information management system that has a function of traceability management has been developed. This information management system standardizes management for qualification documents of medical instruments, and ensures that qualification documents of medical instruments are available and can be traced. Besides, it can reduce the amount of work for medical instruments management.

[Refined Management of the Second Class Warehouse and Cost-benefit Analysis for In-vitro Diagnostic Reagent].

As the material basis of clinical examination, in -vitro diagnostic reagent could directly affect the timeliness and accuracy of clinical examination report if it was not uses properly. This article discusses about how to strengthen the management for the temperature monitoring, effect management, inventory management and cost-benefit analysis of in-vitro diagnostic reagents. An information management system that provides methods for fine management of in-vitro diagnostic reagents has been developed.

[A Medical Devices Management Information System Supporting Full Life-Cycle Process Management].

Medical equipments are essential supplies to carry out medical work. How to ensure the safety and reliability of the medical equipments in diagnosis, and reduce procurement and maintenance costs is a topic of concern to everyone. In this paper, product lifecycle management (PLM) and enterprise resource planning (ERP) are cited to establish a lifecycle management information system. Through integrative and analysis of the various stages of the relevant data in life-cycle, it can ensure safety and reliability of medical equipments in the operation and provide the convincing data for meticulous management.

The management in response to marine oil spill from ships in China: A systematic review.

Historical trends about marine ship-source oil spill incidents from 1990 to 2010 in China were analyzed, and it provided an overview of the status quo of China's management in response to marine oil spill from ships. The Chinese government has issued a series of laws on marine environmental protection since 1982, and promulgated many regulations to prevent and tackle ship-source oil spill. At present, the oil spill emergency response system established in China has five levels: the national level, sea level, provincial level, port level, and ship level. China has demonstrated its ability to control and remove small-scale oil spill from ships in port area and near-shore coastal waters, and also paid attention to related research and development projects. Although China has made significant progress in managing shipping oil spill, challenges still exist, including strengthening oil spill emergency cooperation, enhancing China's response capability, and improving relevant research and development projects.