Investigation of the Microbial Diversity in the Oryza sativa Cultivation Environment and Artificial Transplantation of Microorganisms to Improve Sustainable Mycobiota.

Rice straw is not easy to decompose, it takes a long time to compost, and the anaerobic bacteria involved in the decomposition process produce a large amount of carbon dioxide (CO2), indicating that applications for rice straw need to be developed. Recycling rice straw in agricultural crops is an opportunity to increase the sustainability of grain production. Several studies have shown that the probiotic population gradually decreases in the soil, leading to an increased risk of plant diseases and decreased biomass yield. Because the microorganisms in the soil are related to the growth of plants, when the soil microbial community is imbalanced it seriously affects plant growth. We investigated the feasibility of using composted rice stalks to artificially cultivate microorganisms obtained from the Oryza sativa-planted environment for analyzing the mycobiota and evaluating applications for sustainable agriculture. Microbes obtained from the water-submerged part (group-A) and soil part (group-B) of O. sativa were cultured in an artificial medium, and the microbial diversity was analyzed with internal transcribed spacer sequencing. Paddy field soil was mixed with fermented paddy straw compost, and the microbes obtained from the soil used for O. sativa planting were designated as group-C. The paddy fields transplanted with artificially cultured microbes from group-A were designated as group-D and those from group-B were designated as group-E. We found that fungi and yeasts can be cultured in groups-A and -B. These microbes altered the soil mycobiota in the paddy fields after transplantation in groups-D and -E compared to groups-A and -B. Development in O. sativa post treatment with microbial transplantation was observed in the groups-D and -E compared to group-C. These results showed that artificially cultured microorganisms could be efficiently transplanted into the soil and improve the mycobiota. Phytohormones were involved in improving O. sativa growth and rice yield via the submerged part-derived microbial medium (group-D) or the soil part-derived microbial medium (group-E) treatments. Collectively, these fungi and yeasts may be applied in microbial transplantation via rice straw fermentation to repair soil mycobiota imbalances, facilitating plant growth and sustainable agriculture. These fungi and yeasts may be applied in microbial transplantation to repair soil mycobiota imbalances and sustainable agriculture.

How to Prevent Nerve Root Injury in Uniportal Full Endoscopic Lumbar Fusion Surgery? Insights from a Cadaveric Anatomical Study with Simulation Surgery.

STUDY DESIGN: The study included two fresh-frozen cadavers. OBJECTIVE: To elucidate the positional relationship between surgical instruments and nerve roots during full endoscopic facet-sparing (FE fs-TLIF) and facet-resecting (FE fr-TLIF) lumbar interbody fusion and propose safe instrumentation insertion procedures and recommend cage glider designs aimed at protecting nerve roots. SUMMARY OF BACKGROUND DATA: Endoscopic surgical techniques are increasingly used for minimally invasive lumbar fusion surgery with FE fr-TLIF and FE fs-TLIF being common approaches. However, the risk of nerve root injury remains a significant concern during these procedures. METHODS: Eight experienced endoscopic spine surgeons performed uniportal FE fr-TLIF and FE fs-TLIF on cadaveric lumbar spines, totaling 16 surgeries. Post-operation, soft tissues were removed to assess the positional relationship between the cage entry point and nerve roots. Distances between the cage entry point, traversing nerve root, and exiting nerve root were measured. Safe instrumentation design and insertion procedures were determined. RESULTS: In FE fr-TLIF, the mean distance between the cage entry point and traversing nerve root was significantly shorter compared to FE fs-TLIF (3.30±1.35 mm vs. 8.58±2.47 mm, respectively; P<0.0001). Conversely, the mean distance between the cage entry point and the exiting nerve root was significantly shorter in FE fs-TLIF compared to FE fr-TLIF (3.73±1.97 mm vs. 6.90±1.36 mm, respectively; P<0.0001). For FE fr-TLIF, prioritizing the protection of the traversing root using a two-bevel tip cage glider was crucial. In contrast, for FE fs-TLIF, a single-bevel tip cage glider placed in the caudal location was recommended. CONCLUSION: This study elucidates the anatomical relationship between cage entry points and nerve roots in uniportal endoscopic lumbar fusion surgery. Protection strategies should prioritize the traversing root in FE fr-TLIF and the exiting root in FE fs-TLIF, with corresponding variations in surgical techniques. LEVEL OF EVIDENCE: V.

Pacing Strategies in Elite Individual-Medley Swimmers: A Decision-Tree Approach.

PURPOSE: This study aimed to examine pacing strategies and identify the stroke that has the most significant impact on overall performance in men's and women's 200-m and 400-m individual-medley events from 2000 to 2021. METHODS: The time in each lap and overall race was retrieved from the World Aquatics website. The standardized time for each stroke in individual medley was calculated by dividing the actual time by a reference time specific to each stroke. The reference time was derived from the respective laps in single-stroke finals in the 2017 World Swimming Championships. The decision-tree method was used for analysis. The dependent variables were qualified or nonqualified in heats and semifinals, and winning medals in finals. The independent variables were the ratio of standardized time in each stroke to the sum of standardized time in all 4 strokes. RESULTS: Swimmers who spent a higher ratio of standardized time in the butterfly stroke (>0.236-0.245) are associated with a higher likelihood of winning medals or qualifying for the next stage in most men's and women's 200-m and 400-m individual medley. Butterfly exhibited the highest normalized importance that distinguished medalists from nonmedalists in the finals. The front-crawl stroke is the second most important determinant in medalists in men's and women's 200-m individual medley, whereas backstroke and breaststroke were the second most important in men's and women's 400-m individual medley, respectively. CONCLUSION: Individual-medley swimmers who were excellent in butterfly and conserved energy in butterfly had a higher likelihood of success.

Administration of N-Acetylcysteine to Regress the Fibrogenic and Proinflammatory Effects of Oxidative Stress in Hypertrophic Ligamentum Flavum Cells.

Ligamentum flavum hypertrophy (LFH) is a major cause of lumbar spinal stenosis (LSS). In hypertrophic ligamentum flavum (LF) cells, oxidative stress activates intracellular signaling and induces the expression of inflammatory and fibrotic markers. This study explored whether healthy and hypertrophic LF cells respond differently to oxidative stress, via examining the levels of phosphorylated p38 (p-p38), inducible nitric oxide synthase (iNOS), and α-smooth muscle actin (α-SMA). Furthermore, the efficacy of N-acetylcysteine (NAC), an antioxidant, in reversing the fibrogenic and proinflammatory effects of oxidative stress in hypertrophic LF cells was investigated by assessing the expression levels of p-p38, p-p65, iNOS, TGF-ß, α-SMA, vimentin, and collagen I under H2O2 treatment with or without NAC. Under oxidative stress, p-p38 increased significantly in both hypertrophic and healthy LF cells, and iNOS was elevated in only the hypertrophic LF cells. This revealed that oxidative stress negatively affected both hypertrophic and healthy LF cells, with the hypertrophic LF cells exhibiting more active inflammation than did the healthy cells. After H2O2 treatment, p-p38, p-p65, iNOS, TGF-ß, vimentin, and collagen I increased significantly, and NAC administration reversed the effects of oxidative stress. These results can form the basis of a novel therapeutic treatment for LFH using antioxidants.

How platinum-induced nephrotoxicity occurs? Machine learning prediction in non-small cell lung cancer patients.

BACKGROUND AND OBJECTIVE: Platinum-induced nephrotoxicity is a severe and unexpected adverse drug reaction that could lead to treatment failure in non-small cell lung cancer patients. Better prediction and management of this nephrotoxicity can increase patient survival. Our study aimed to build up and compare the best machine learning models with clinical and genomic features to predict platinum-induced nephrotoxicity in non-small cell lung cancer patients. METHODS: Clinical and genomic data of patients undergoing platinum chemotherapy at Wan Fang Hospital were collected after they were recruited. Twelve models were established by artificial neural network, logistic regression, random forest, and support vector machine with integrated, clinical, and genomic modes. Grid search and genetic algorithm were applied to construct the fine-tuned model with the best combination of predictive hyperparameters and features. Accuracy, precision, recall, F1 score, and area under the receiver operating characteristic curve were calculated to compare the performance of the 12 models. RESULTS: In total, 118 patients were recruited for this study, among which 28 (23.73%) were experiencing nephrotoxicity. Machine learning models with clinical and genomic features achieved better prediction performances than clinical or genomic features alone. Artificial neural network with clinical and genomic features demonstrated the best predictive outcomes among all 12 models. The average accuracy, precision, recall, F1 score and area under the receiver operating characteristic curve of the artificial neural network with integrated mode were 0.923, 0.950, 0.713, 0.808 and 0.900, respectively. CONCLUSIONS: Machine learning models with clinical and genomic features can be a preliminary tool for oncologists to predict platinum-induced nephrotoxicity and provide preventive strategies in advance.

Retention modeling and adsorption mechanisms in reversed-phase liquid chromatography.

To interpret the dependence of solute retention behavior on modifier content in reversed-phase liquid chromatography, a theoretical framework, based on the concentration dependence of solvophobic forces imposed on solutes and the competitive adsorptions of solutes and solvent modifiers, was proposed. The generality of the developed model was demonstrated by comparing the model with conventional retention models. The linear dependence of the Gibbs energy change of solute adsorption with respect to the modifier concentration was assumed, and the model was fitted to the experimental results, with good agreement demonstrated between the experimental data and the model. Retention behaviors were inferred to be determined by two key dimensionless groups that represented the reductions in the retention factors resulting from a weakened solvophobic interaction and modifier competitive adsorption. The retention behaviors were successfully deconvoluted for each contribution as a function of the modifier concentration by using the fitted parameters. The effects of both contributions on the retention behaviors were enhanced for the solutes with aromatic groups. The standard Gibbs energy change SLo of benzene adsorption was found to depend linearly on the number of modifier molecules present but independent of modifier identity. For the solutes associated with hydrogen-bonding groups, the degree of reduction in the solvophobic interactions was considerably reduced. Hence, the relative contributions of both mechanisms to solute retention depend greatly on the solute structure. Perturbation method was performed to investigate the modifier adsorption mechanisms. The results show that the standard Gibbs energy change SLo for the first-layer adsorption of modifiers changed linearly with the carbon number of modifier molecule. These results demonstrated that the proposed model can offer a physically consistent quantitative description of retention when solvent composition is varied.

Submergence Gene Sub1A Transfer into Drought-Tolerant japonica Rice DT3 Using Marker-Assisted Selection.

Flash flooding is a major environmental stressor affecting rice production worldwide. DT3 is a drought-tolerant, recurrent parent with a good yield, edible quality, and agronomic traits akin to those of an elite Taiwanese variety, Taiken9 (TK9). Progenies carrying Sub1A can enhance submergence stress tolerance and can be selected using the marker-assisted backcross (MAB) breeding method. For foreground selection, Sub1A and SubAB1 were utilized as markers on the BC2F1, BC3F1, and BC3F2 generations to select the submergence-tolerant gene, Sub1A. Background selection was performed in the Sub1A-BC3F2 genotypes, and the percentages of recurrent parent recovery within individuals ranged from 84.7-99.55%. BC3F3 genotypes (N = 100) were evaluated for agronomic traits, yield, and eating quality. Four of the eleven BC3F4 lines showed good yield, yield component, grain, and eating quality. Four BC3F4 lines, SU39, SU40, SU89, and SU92, exhibited desirable agronomic traits, including grain quality and palatability, consistent with those of DT3. These genotypes displayed a high survival rate between 92 and 96%, much better compared with DT3 with 64%, and demonstrated better drought tolerance compared to IR64 and IR96321-345-240. This study provides an efficient and precise MAB strategy for developing climate-resilient rice varieties with good grain quality for flood-prone regions.

Pyramiding Bacterial Blight Resistance Genes in Tainung82 for Broad-Spectrum Resistance Using Marker-Assisted Selection.

Tainung82 (TNG82) is one of the most popular japonica varieties in Taiwan due to its relatively high yield and grain quality, however, TNG82 is susceptible to bacterial blight (BB) disease. The most economical and eco-friendly way to control BB disease in japonica is through the utilization of varieties that are resistant to the disease. In order to improve TNG82's resistance to BB disease, five bacterial blight resistance genes (Xa4, xa5, Xa7, xa13 and Xa21) were derived from a donor parent, IRBB66 and transferred into TNG82 via marker-assisted backcrossing breeding. Five BB-resistant gene-linked markers were integrated into the backcross breeding program in order to identify individuals possessing the five identified BB-resistant genes (Xa4, xa5, Xa7, xa13 and Xa21). The polymorphic markers between the donor and recurrent parent were used for background selection. Plants having maximum contribution from the recurrent parent genome were selected in each generation and crossed with the recipient parent. Selected BC3F1 plants were selfed in order to generate homozygous BC3F2 plants. Nine pyramided plants, possessing all five BB-resistant genes, were obtained. These individuals displayed a high level of resistance against the BB strain, XF89-b. Different BB gene pyramiding lines were also inoculated against the BB pathogen, resulting in more than three gene pyramided lines that exhibited high levels of resistance. The five identified BB gene pyramided lines exhibited yield levels and other desirable agronomic traits, including grain quality and palatability, consistent with TNG82. Bacterial blight-resistant lines possessing the five identified BB genes exhibited not only higher levels of resistance to the disease, but also greater yield levels and grain quality. Pyramiding multiple genes with potential characteristics into a single genotype through marker-assisted selection can improve the efficiency of generating new crop varieties exhibiting disease resistance, as well as other desirable traits.

Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza.

Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups. The subgroup RTPOSON_sub3 had the smallest DNA size and 97% (32/33) of RTPOSON elements from Oryza punctata are classified in this group. The insertion time of these RTPOSONs varied and their proliferation occurred within the last 8 Mya, with two bursting periods within the last 1.5-5.0 Mya. A total of 37 different orthologous insertions of RTPOSONs, with different nested transposable elements and gene fragments, were identified by comparing the genomes of ssp. japonica cv. Nipponbare and ssp. indica cv. 93-11. A part of intact RTPOSON elements was evolved independently after the divergence of indica and japonica. In addition, intact RTPOSONs and homologous fragments were preferentially retained or integrated in genic regions. This novel LTR retrotransposon, RTPOSON, might have an impact on genome evolution, genic innovation, and genetic variation.

Genetic factors responsible for eating and cooking qualities of rice grains in a recombinant inbred population of an inter-subspecific cross.

The eating and cooking qualities of rice grains are the major determinants of consumer preference and, consequently, the economic value of a specific rice variety. These two qualities are largely determined by the physicochemical properties of the starch, i.e. the starch composition, of the rice grain. In our study, we determined the genetic factors responsible for the physicochemical properties of starch in recombinant inbred lines (RILs) of japonica cv. Tainung 78 × indica cv. Taichung Sen 17 (TCS 17) cultivated over two crop seasons by examining palatability characteristics and several Rapid Viscosity Analyzer (RVA) parameters. Thirty-four quantitative trait loci (QTLs), each explaining between 1.2 and 78.1 % phenotypic variation, were mapped in clusters on eight chromosomes in 190 RILs genotyped with 139 markers. Ten pairs of QTLs were detected in the two environments, of which seven were in agreement with previous findings, suggesting that these QTLs may express stable experimental populations across various environments. Waxy (Wx), which controls amylose synthesis, was determined to be a primary gene regulating the physicochemical properties of cooked rice grains, as indicated by the presence of a major QTL cluster on chromosome 6 and by marker regression analysis. Six starch synthesis-related genes (SSRGs) which were located in the QTL intervals significantly differed in terms of gene expression between the two parents during grain-filling and were important genetic factors affecting physicochemical properties. The expression of four genes, PUL, ISA2, GBSSI, and SSII-3, was significantly upregulated in TCS 17, and this expression was positively correlated with six traits. The effects of the six SSRGs and gene interaction depended on genetic background and environment; grain quality may be fine tuned by selecting for SBE4 for japonica and PUL for indica. We provide valuable information for application in the breeding of new rice varieties as daily staple food and for use in industrial manufacturing by marker-assisted selection.

Stereocontrolled synthesis of complicated oxacyclic compounds via platinum-catalyzed [4 + 2]-cycloadditions and annulations of enynals with allylic alcohols.

We report stereoselective synthesis of tricyclic ketals through Pt(II)-catalyzed [4 + 2]-cycloaddition of benzopyrilium/1-en-3-ol functionalities. For nonaromatic enynals, we obtained distinct tricyclic oxacyclic ketones due to occurrence of a new annulation reaction. This work reports the first example that [4 + 2]-cycloadducts are successfully intercepted from such functionalities in diversified approaches. The value of such cycloadditions and annulations are shown by their high diastereoselectivities and chemoselectivities.

Gold-catalyzed [4+3]-annulation of oxabicyclic benzenes with 2-substituted allylsilanes through tandem allylation and cyclization.

This work reports new gold-catalyzed [4+3]-annulations of oxacyclic benzenes with 2-substituted allylsilanes through tandem allylation and cyclization; on the basis of experimental observations, we propose a mechanism involving the opening of the oxacyclic ring by a PPh3Au+-assisted SN2-attack of allylsilanes.