Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics.

A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein-protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop-pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.

Genomic variation in 3,010 diverse accessions of Asian cultivated rice.

Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.

Engineering broad-spectrum resistance to rice bacterial blight by editing the OsETR susceptible haplotype using CRISPR/Cas9.

KEY MESSAGE: CRISPR/Cas9-mediated knockout of the susceptible haplotype of OsETR, encoding an embryogenesis transmembrane protein, confers broad-spectrum resistance to bacterial leaf blight in a susceptible rice cultivar without yield penalty.

R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation.

R-loops play versatile roles in many physiological and pathological processes, and are of great interest to scientists in multiple fields. However, controversy about their genomic localization and incomplete understanding of their regulatory network raise great challenges for R-loop research. Here, we present R-loopBase (https://rloopbase.nju.edu.cn) to tackle these pressing issues by systematic integration of genomics and literature data. First, based on 107 high-quality genome-wide R-loop mapping datasets generated by 11 different technologies, we present a reference set of human R-loop zones for high-confidence R-loop localization, and spot conservative genomic features associated with R-loop formation. Second, through literature mining and multi-omics analyses, we curate the most comprehensive list of R-loop regulatory proteins and their targeted R-loops in multiple species to date. These efforts help reveal a global regulatory network of R-loop dynamics and its potential links to the development of cancers and neurological diseases. Finally, we integrate billions of functional genomic annotations, and develop interactive interfaces to search, visualize, download and analyze R-loops and R-loop regulators in a well-annotated genomic context. R-loopBase allows all users, including those with little bioinformatics background to utilize these data for their own research. We anticipate R-loopBase will become a one-stop resource for the R-loop community.

The efficacy of orthokeratology lenses with smaller back optic zone diameter in myopia control. A meta-analysis.

PURPOSE: This study was conducted to determine whether orthokeratology (OK) lenses with a smaller back optic zone diameter (BOZD) could exhibit stronger myopia control effects. METHOD: A meta-analysis was registered in PROSPERO (CRD42023408184). A comprehensive systematic database search was conducted, encompassing PubMed, Cochrane Library, EMBASE, MEDLINE, Web of Science, Ovid, CNKI and CBM, to identify relevant studies up to 25 March 2023. The primary inclusion criteria for this meta-analysis were studies that investigated the myopia control effect of OK lenses with a small optical treatment area (≤5 mm). To assess the quality of the retrieved articles, two researchers evaluated them using the Cochrane bias risk assessment criteria. The primary outcome measures were the changes in axial length (AL) and refractive error, using the weighted mean differences (WMD) and 95% confidence intervals (CI) to assess differences between small and traditional back optical treatment zone groups in terms of these outcomes. RESULTS: The analysis encompassed five eligible studies, with a 1 year duration. The average difference in AL between the groups was 0.12 mm (WMD = -0.12, 95% CI [-0.16, -0.09], p < 0.00001). Likewise, the average difference in refractive error between the two groups was 0.44 D (WMD = 0.44, 95% CI [0.30, 0.57], p < 0.00001). None of the studies reported severe adverse events. CONCLUSIONS: Current evidence suggests that OK lenses with smaller back optical treatment zone are more effective in preventing myopia progression than traditional lenses. However, a longer-term evaluation is warranted.

Artificial Intelligence-Assisted Prescription Determination for Orthokeratology Lens Fitting: From Algorithm to Clinical Practice.

OBJECTIVES: To explore the potential of artificial intelligence (AI) to assist prescription determination for orthokeratology (OK) lenses. METHODS: Artificial intelligence algorithm development followed by a real-world trial. A total of 11,502 OK lenses fitting records collected from seven clinical environments covering major brands. Records were randomly divided in a three-way data split. Cross-validation was used to identify the most accurate algorithm, followed by an evaluation using an independent test data set. An online AI-assisted system was implemented and assessed in a real-world trial involving four junior and three senior clinicians. RESULTS: The primary outcome measure was the algorithm's accuracy (ACC). The ACC of the best performance of algorithms to predict the targeted reduction amplitude, lens diameter, and alignment curve of the prescription was 0.80, 0.82, and 0.83, respectively. With the assistance of the AI system, the number of trials required to determine the final prescription significantly decreased for six of the seven participating clinicians (all P <0.01). This reduction was more significant among junior clinicians compared with consultants (0.76±0.60 vs. 0.32±0.60, P <0.001). Junior clinicians achieved clinical outcomes comparable to their seniors, as 93.96% (140/149) and 94.44% (119/126), respectively, of the eyes fitted achieved unaided visual acuity no worse than 0.8 ( P =0.864). CONCLUSIONS: AI can improve prescription efficiency and reduce discrepancies in clinical outcomes among clinicians with differing levels of experience. Embedment of AI in practice should ultimately help lessen the medical burden and improve service quality for myopia boom emerging worldwide.

Genome-Wide Association Study Identifies Resistance Loci for Bacterial Blight in a Collection of Asian Temperate Japonica Rice Germplasm.

Growing resistant rice cultivars is the most effective strategy to control bacterial blight (BB), a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo). Screening resistant germplasm and identifying resistance (R) genes are prerequisites for breeding resistant rice cultivars. We conducted a genome-wide association study (GWAS) to detect quantitative trait loci (QTL) associated with BB resistance using 359 East Asian temperate Japonica accessions inoculated with two Chinese Xoo strains (KS6-6 and GV) and one Philippine Xoo strain (PXO99A). Based on the 55K SNPs Array dataset of the 359 Japonica accessions, eight QTL were identified on rice chromosomes 1, 2, 4, 10, and 11. Four of the QTL coincided with previously reported QTL, and four were novel loci. Six R genes were localized in the qBBV-11.1, qBBV-11.2, and qBBV-11.3 loci on chromosome 11 in this Japonica collection. Haplotype analysis revealed candidate genes associated with BB resistance in each QTL. Notably, LOC_Os11g47290 in qBBV-11.3, encoding a leucine-rich repeat receptor-like kinase, was a candidate gene associated with resistance to the virulent strain GV. Knockout mutants of Nipponbare with the susceptible haplotype of LOC_Os11g47290 exhibited significantly improved BB resistance. These results will be useful for cloning BB resistance genes and breeding resistant rice cultivars.

Patient-centred care and patient autonomy: doctors' views in Chinese hospitals.

BACKGROUND: Patient-centred care and patient autonomy is one of the key factors to better quality of service provision, hence patient outcomes. It enables the development of patients' trusts which is an important element to a better doctor-patient relationship. Given the increasing number of patient disputes and conflicts between patients and doctors in Chinese public hospital, it is timely to ensure patient-centred care is fully and successfully implemented. However, limited studies have examined the views and practice in different aspects of patient-centred care among doctors in the Chinese public hospitals. METHODS: A quantitative approach was adopted by distributing paper-based questionnaires to doctors and patients in two hospitals (Level III and Level II) in Jinan, Shandong province, China. RESULTS: In total, 614 doctors from the surgical and internal medicine units of the two hospitals participated in the survey yielding 90% response rates. The study confirmed the inconsistent views among doctors in terms of their perception and practice in various aspects patient-centred care and patient autonomy regardless of the hospital where they work (category II or category III), their unit speciality (surgical or non-surgical), their gender or seniority. The high proportion of doctors (more than 20%) who did not perceive the importance of patient consultation prior to determining diagnostic and treatment procedure is alarming. This in in part due to the belief held by more than half of the doctors that patients were unable to make rational decisions and their involvement in treatment planning process did not necessarily lead to better treatment outcomes. CONCLUSION: The study calls for the development of system level policy and organisation wide strategies in encouraging and enabling the practice of patient-centred care and patient autonomy with the purposes of improving the quality of the service provided to patients by Chinese hospitals.

Performance-Enhancing Approaches for PEDOT:PSS-Si Hybrid Solar Cells.

The emerging energy crisis has focused significant worldwide attention on solar cells. Although crystalline silicon solar cells are currently widely used, their high cost limits the development of solar power generation. Consequently, hybrid solar cells are becoming increasingly important, especially organic-Si hybrid solar cells (HSCs). Organic-Si HSCs combine a mature technology and high efficiency with the low-temperature manufacturing process and tunable optoelectronic properties of organic solar cells. The organic material can be P3HT, carbon nanotubes, graphene, and PEDOT:PSS. Here we review the performance of PEDOT:PSS/Si HSCs and methods for improving their efficiency, such as PEDOT:PSS modification, optimization of the trapping effect, passivation of the silicon surface, addition of an interface layer, improvement of a back contact, and optimization of the metal top electrode. This Review should help fill the gap in this area and provide perspectives for the future development of the PEDOT:PSS/Si HSCs.

Comparative proteomic analysis reveals novel insights into the interaction between rice and Xanthomonas oryzae pv. oryzae.

BACKGROUND: Bacterial blight, which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Rice introgression line H471, derived from the recurrent parent Huang-Hua-Zhan (HHZ) and the donor parent PSBRC28, exhibits broad-spectrum resistance to Xoo, including to the highly virulent Xoo strain PXO99A, whereas its parents are susceptible to PXO99A. To characterize the responses to Xoo, we compared the proteome profiles of the host and pathogen in the incompatible interaction (H471 inoculated with PXO99A) and the compatible interaction (HHZ inoculated with PXO99A). RESULTS: In this study, a total of 374 rice differentially abundant proteins (DAPs) and 117 Xoo DAPs were detected in the comparison between H471 + PXO99A and HHZ + PXO99A. Most of the Xoo DAPs related to pathogen virulence, including the outer member proteins, type III secretion system proteins, TonB-dependent receptors, and transcription activator-like effectors, were less abundant in the incompatible interaction than in the compatible interaction. The rice DAPs were mainly involved in secondary metabolic processes, including phenylalanine metabolism and the biosynthesis of flavonoids and phenylpropanoids. Additionally, some DAPs involved in the phenolic phytoalexin and salicylic acid (SA) biosynthetic pathways accumulated much more in H471 than in HHZ after the inoculation with PXO99A, suggesting that phytoalexin and SA productions were induced faster in H471 than in HHZ. Further analyses revealed that the SA content increased much more rapidly in H471 than in HHZ after the inoculation, suggesting that the SA signaling pathway was activated faster in the incompatible interaction than in the compatible interaction. CONCLUSIONS: Overall, our results indicate that during an incompatible interaction between H471 and PXO99A, rice plants prevent pathogen invasion and also initiate multi-component defense responses that inhibit disease development.

Association of methylenetetrahydrofolate reductase (MTHFR) variant C677T and risk of carotid atherosclerosis: a cross-sectional analysis of 730 Chinese Han adults in Chongqing.

BACKGROUND: Uncertainty still remains on the correlation of methylenetetrahydrofolate reductase (MTHFR) variant C677T with risk of carotid atherosclerosis (CAS), and there is a lack of reports on C677T/MTHFR in the Asian population. The association of C677T/MTHFR polymorphisms with CAS in the Chinese Han population in Chongqing was investigated in the present study. METHODS: Subjects (n = 730, 214 females and 516 males, Han ethnicity) who provided an informed consent were randomly selected from the general population of Chongqing, China. Polymerase chain reaction-restriction fragment length polymorphism and Sanger sequencing genotyping assays were used to determine the MTHFR genotypes. The atherosclerosis index of the intima-media thickness (IMT) was measured by high-resolution ultrasound to evaluate the CAS. Less than 1.0 mm was considered as normal for IMT, 1.0-1.5 mm was considered as thickening, and ≥ 1.5 mm and a local bulge thickened in the lumen was considered as CAS. According to the carotid ultrasonography results, these subjects were divided into two groups: CAS-group (IMT ≥ 1.0 mm) and control group (IMT < 1.0 mm). RESULTS: The frequency of C/T heterozygotes, T/T homozygotes genotype was significantly higher in the subjects with CAS (62% vs. 36.9%; 16.2% vs. 9.5%; 47.2% vs. 27.9%, P < 0.05), while the frequency of C/C homozygotes and C allele was significantly lower (21.8% vs. 53.7%; 52.8% vs. 72.1%, P < 0.05), when compared to the control group. The risk of CAS was higher for subjects with C/T heterozygotes and T/T homozygotes (OR = 4.06, 95% CI: 2.76-5.98, P < 0.001 and OR = 3.14, 95% CI: 1.73-5.69, P < 0.001, respectively), when compared to the subjects with the C/C genotype. In the model 1 (CT + TT versus CC), C677T/MTHFR was significantly associated with the prevalence of CAS, and the all adjusted OR values for CAS were 3.87 (95% CI, 2.67 to 5.62) in all, 17.18 (95% CI, 7.27 to 40.49) in women and 2.57 (95% CI, 1.65 to 3.99) in men after adjusting for potential confounding factors. CONCLUSIONS: The present study suggests that a mutation in the methylenetetrahydrofolate reductase gene is a risk factor of CAS in the Chinese Han population.

Doctors in Chinese public hospitals: demonstration of their professional identities.

BACKGROUND: An increase in the number of medical disputes and violence against doctors indicates a lack of trust in the medical profession by society in Chinese public hospitals. Empirical evidence confirms that one cause is the lack of professional identity demonstrated by doctors. Medical professionals are required to maintain high standards of competence and moral responsibility, and demonstrate qualities such as respect, compassion, integrity, responsiveness to needs, and commitment to sound ethical practice in order to maintain professional privilege. These principles and appropriate professional conduct are the foundation of the professional identity of the medical profession. METHODS: A quantitative approach was adopted by distributing paper-based questionnaires to doctors and patients in two hospitals (Level III and Level II) in Jinan, Shandong province, China. FINDINGS: In total, 614 doctors and 1184 inpatients on discharge from the surgical and internal medicine units of the two hospitals participated in the survey yielding 90% response rates. The study confirmed the variation amongst doctors in demonstrating their professionalism in terms of respecting patients' views and preferences when determining diagnostic procedures and treatment plans, and when making ethical decisions. Although 90% patients indicated that they showed respects to doctors, close to 20% of the doctors disagreed that they received high respect from patients. About 12% of doctors prescribed unnecessary diagnostic procedures to patient for the purpose of generating profit and more than 20% of patients indicated that they gave gifts to doctors in order to receive better treatment. CONCLUSIONS: Although about 80% of doctors demonstrated certain aspects of professionalism required by practitioners, the inconsistency across the medical workforce may exacerbate tense doctor-patient relationships. A review of medical curricula and focus of the internship program is required in order to assist medical graduates with forming required professional identity in order to improve patient satisfaction and better clinical outcomes. To be effective, a more systematic approach is recommended.

Mercury Concentrations and Se:Hg Molar Ratios in Flyingfish (Exocoetus volitans) and Squid (Uroteuthis chinensis).

We measured total mercury (Hg) and selenium (Se) concentrations as well as stable nitrogen (N) isotopic composition in flyingfish and squid muscle tissues from the eastern Indian Ocean and western South China Sea. The results showed that the mean Hg concentration in squid muscle from the western South China Sea was lower than that in the eastern Indian Ocean. The Hg concentrations in flyingfish and squid muscle samples were positively correlated with organism size (length and weight) and δ15N in all the study areas. Furthermore, we found a negative correlation between Se and Hg in molar content of flyingfish and squid muscle from the western South China Sea. The Se:Hg molar ratio was significantly negative correlated with fish weight and δ15N, suggesting that the Se:Hg molar ratio decreases with the increase of fish size and trophic level in the food web.

Genome-wide association study of salt tolerance at the seed germination stage in rice.

BACKGROUND: Improving the salt tolerance of direct-seeding rice at the seed germination stage is a major breeding goal in many Asian rice-growing countries, where seedlings must often establish in soils with a high salt content. Thus, it is important to understand the genetic mechanisms of salt tolerance in rice and to screen for germplasm with salt tolerance at the seed germination stage. Here, we investigated seven seed germination-related traits under control and salt-stress conditions and conducted a genome-wide association study based on the re-sequencing of 478 diverse rice accessions. RESULTS: The analysis used a mixed linear model and was based on 6,361,920 single nucleotide polymorphisms in 478 rice accessions grouped into whole, indica, and non-indica panels. Eleven loci containing 22 significant salt tolerance-associated single nucleotide polymorphisms were identified based on the stress-susceptibility indices (SSIs) of vigor index (VI) and mean germination time (MGT). From the SSI of VI, six major loci were identified, explaining 20.2% of the phenotypic variation. From the SSI of MGT, five major loci were detected, explaining 26.4% of the phenotypic variation. Of these, seven loci on chromosomes 1, 5, 6, 11, and 12 were close to six previously identified quantitative gene loci/genes related to tolerance to salinity or other abiotic stresses. The strongest association region for the SSI of MGT was identified in a ~ 13.3 kb interval (15450039-15,463,330) on chromosome 1, near salt-tolerance quantitative trait loci controlling the Na+: K+ ratio, total Na+ uptake, and total K+ concentration. The strongest association region for the SSI of VI was detected in a ~ 164.2 kb interval (526662-690,854) on chromosome 2 harboring two nitrate transporter family genes (OsNRT2.1 and OsNRT2.2), which affect gene expression under salt stress. The haplotype analysis indicated that OsNRT2.2 was associated with subpopulation differentiation and its minor/rare tolerant haplotype was detected. CONCLUSIONS: These results provide valuable information for salt tolerance-related gene cloning and for understanding the genetic mechanisms of salt tolerance at the seed germination stage. This information will be useful to improve the salt tolerance of direct-seeding rice varieties by genomic selection or marker-assisted selection.

[Diagnosis of Argon Metastable State in Low Pressure DBD Plasma Using Diode Laser Absorption Spectroscopy].

Gas temperature and density of Ar metastable state in DBD Ar (Ar/N(2)) plasma were measured using the tunable diode-laser absorption spectroscopy technology at low pressure. The variation trend of the densities of Ar metastable state 1s(5), 1s(3) and gas temperature with voltage, pressure, gas flow, electrode distance and N(2) concentration was studied. The density of Ar metastable was obtained by calculating the absorption peak area of absorption line based on the Lambert-Beer law, while gas temperature was determined with Doppler width of the absorption line in Voigt fitting. We deduced that the main source of the Ar metastable was the electron-impact excitation from the ground state, and the main loss process was the electron quenching. In addition, the actual discharge power, the electron state and the collision between particles were responsible for the variation of gas temperature. It was found that, when the voltage and gas flow increasing, both temperature and densities of 1s(5), 1s(3) shown the similar trends, which increasing rapidly at first and then slowly. In addition, the variation with gas flow was smaller than that with gas flow. With pressure increasing, temperature and densities of 1s(5), 1s(3) increased till to a max value and then decreased. Meanwhile, the experimental data indicated that the pressure had a greater effect on spectral line width. To increase the electrode distance properly, the density of 1s(5), 1s(3) decreased while the gas temperature increased. N(2) added to Ar presented a great negative effect on the density of Ar metastable state. Even 0.5% N(2) added to Ar, the densities of 1s(5) and 1s(3) decreased rapidly about to 50%, but then more N(2) added, there was no obvious decrease about density.

Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response.

BACKGROUND: Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Xa39 is a resistance (R) gene with a broad-spectrum hypersensitive response (BSHR) to Xoo. Nevertheless, the molecular mechanisms of resistance mediated by Xa39 remain unclear. In this study, the transcriptome profiling of a rice line carrying Xa39 and its parents at the early stage of Xoo infection were investigated. RESULTS: A rice introgression line H471 carrying Xa39 exhibited a typical local hypersensitive response phenotype, accompanied by programmed cell death after inoculation with the Xoo Philippines' race 9b. Transcriptome profiling of H471 and its parents at 1 and 2 days post-inoculation was performed using RNA sequencing. In total, 306 differentially expressed genes (DEGs) were identified in H471 compared with its recurrent parent Huang-Hua-Zhan after inoculation with Xoo. Among them, 121 (39.5%) genes, with functional enrichments that were related to defense response, protein amino acid phosphorylation, and apoptosis, were found to be constitutively expressed. The other 185 (60.5%) genes, with GO terms that belonged to defense response, were significantly responsive to Xoo infection in H471. Ten up-regulated and 12 down-regulated genes encoding intracellular immune receptors were identified in H471 compared with Huang-Hua-Zhan. LOC_Os11g37759, which was located in the fine-mapping region harboring Xa39, is a Xa39 candidate gene. The putative BSHR-related co-regulatory networks were constructed using 33 DEGs from four functional groups, including gibberellic acid receptors and brassinosteroid regulators, which were differentially co-expressed with LOC_Os11g37759 in infected H471. Our results indicated that there might be cross-talk between the Xa39-mediated signal transduction cascades and the GA/BR signaling pathway, and that the defense mechanism was related to diverse kinases, transcription factors, post-translational regulation, and R genes. CONCLUSIONS: The present study provides the comprehensive transcriptome profile of a rice introgression line carrying Xa39 and its parents, and identifies a set of DEGs involved in BSHR mediated by Xa39. These data provide novel insights into the regulatory networks of plant disease resistance mediated by R genes, and the identified DEGs will serve as candidates for Xa39 cloning and for further understanding the molecular mechanism of BSHR.

Piezo-Phototronic Effect Controlled Dual-Channel Visible light Communication (PVLC) Using InGaN/GaN Multiquantum Well Nanopillars.

Visible light communication (VLC) simultaneously provides illumination and communication via light emitting diodes (LEDs). Keeping a low bit error rate is essential to communication quality, and holding a stable brightness level is pivotal for illumination function. For the first time, a piezo-phototronic effect controlled visible light communication (PVLC) system based on InGaN/GaN multiquantum wells nanopillars is demonstrated, in which the information is coded by mechanical straining. This approach of force coding is also instrumental to avoid LED blinks, which has less impact on illumination and is much safer to eyes than electrical on/off VLC. The two-channel transmission mode of the system here shows great superiority in error self-validation and error self-elimination in comparison to VLC. This two-channel PVLC system provides a suitable way to carry out noncontact, reliable communication under complex circumstances.

Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress.

BACKGROUND: Rice (Oryza sativa. L) is more sensitive to drought stress than other cereals, and large genotypic variation in drought tolerance (DT) exists within the cultivated rice gene pool and its wild relatives. Selective introgression of DT donor segments into a drought-sensitive (DS) elite recurrent parent by backcrossing is an effective way to improve drought stress tolerance in rice. To dissect the molecular mechanisms underlying DT in rice, deep transcriptome sequencing was used to investigate transcriptome differences among a DT introgression line H471, the DT donor P28, and the drought-sensitive, recurrent parent HHZ under drought stress. RESULTS: The results revealed constitutively differential gene expression before stress and distinct global transcriptome reprogramming among the three genotypes under a time series of drought stress, consistent with their different genotypes and DT phenotypes. A set of genes with higher basal expression in both H471 and P28 compared with HHZ were functionally enriched in oxidoreductase and lyase activities, implying their positive role in intrinsic DT. Gene Ontology analysis indicated that common up-regulated genes in all three genotypes under mild drought stress were enriched in signaling transduction and transcription regulation. Meanwhile, diverse functional categories were characterized for the commonly drought-induced genes in response to severe drought stress. Further comparative transcriptome analysis between H471 and HHZ under drought stress found that introgression caused wide-range gene expression changes; most of the differentially expressed genes (DEGs) in H471 relative to HHZ under drought were beyond the identified introgressed regions, implying that introgression resulted in novel changes in expression. Co-expression analysis of these DEGs represented a complex regulatory network, including the jasmonic acid and gibberellin pathway, involved in drought stress tolerance in H471. CONCLUSIONS: Comprehensive gene expression profiles revealed that genotype-specific drought induced genes and genes with higher expression in the DT genotype under normal and drought conditions contribute jointly to DT improvement. The molecular genetic pathways of drought stress tolerance uncovered in this study, as well as the DEGs co-localized with DT-related QTLs and introgressed intervals, will serve as useful resources for further functional dissection of the molecular mechanisms of drought stress response in rice.

The efficacy of a device-based approach to microorganism disinfection and protein removal for orthokeratology lenses in varied clinical circumstances.

PURPOSE: RigidCare is an electrolysis-based device that recently obtained approval from the US's FDA to sterilise microorganisms and remove proteins for orthokeratology (O-K) lenses. The study was conducted to investigate the device's performance in varied clinical circumstances. METHODS: Trial lenses and private lenses were employed by O-K lens wearers from five hospitals for an evaluation of disinfection and sterilisation and an assessment of protein removal, respectively. Menicon multipurpose solution and protein remover were selected for use with the control group. Following the instructions, pre-cleaning lens samples, post-cleaning lens samples and residual solution samples of trial lenses of the experimental and control groups were collected for microorganism examinations by an experienced third-party testing organisation. The levels of protein deposition for these two approaches were rated by senior O-K experts. Categorical variables were analysed using statistical tests, such as the chi-squared test and Fisher's exact test. RESULTS: The microbial positive rate detected from the pre-cleaning and post-cleaning lens samples and the residual solution of the trial lenses for the experimental and control group was 4/76 vs 1/74 (P = 0.37), 1/76 vs 0/74 (P = 1.00) and 0/76 vs 8/74 (P = 0.006), respectively. Following protein removal, the experimental group exhibited a significantly higher overall proportion of lenses rated as 'clean' or with a 'mild deposit' (96.4 %, 79/82) compared to the control group (85.7 %, 66/77), with a significant difference (P < 0.05). CONCLUSION: This multi-center study demonstrated that RigidCare exhibited superior efficacy in disinfection, sterilisation and protein removal as compared to Menicon multipurpose solution and protein remover.

Pedigree genome data of an early-matured Geng/japonica glutinous rice mega variety Longgeng 57.

By using PacBio HiFi technology, we produced over 700 Gb of long-read sequencing (LRS) raw data; and by using Illumina paired-end whole-genome shotgun (WGS) sequencing technology, we generated more than 70 Gb of short-read sequencing (SRS) data. With LRS data, we assembled one genome and then generate a set of annotation data for an early-matured Geng/japonica glutinous rice mega variety genome, Longgeng 57 (LG57), which carries multiple elite traits including good grain quality and wide adaptability. Together with the SRS data from three parents of LG57, pedigree genome variations were called for three representative types of genes. These data sets can be used for deep variation mining, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general.