Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice

Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.

3D limit analysis of rock slopes based on equivalent linear failure criterion with tension cut-off

Hoek-Brown (HB) failure criterion is widely used to predict the strength of intact or heavily jointed rock mass. For stability analysis of rock slopes governed by the HB failure criterion, the equivalent linearity to Mohr-Coulomb (MC) criterion is often adopted, leading to the well-known equivalent Mohr-Coulomb method (EMCM). Existing studies on EMCM analysis mainly consider the shear strength of rock material, while consideration of the tensile strength is rare. This contradicts the fact that the underlying tensile strength of rock mass has considerable impact on the rock slope stability in real world. In this regard, this paper proposes a limit analysis-based approach that can account for tension in the three-dimensional (3D) stability analysis of HB rock slope. This approach is established on the equivalent linearity of the HB criterion with consideration of tensile strength, known as the equivalent tension cut-off MC method (ETMCM), and using a horn-like 3D mechanism of limit analysis. The safety factor solutions given by the proposed approach are validated by previous studies and numerical results. Parametric studies are conducted to investigate the effect of rock tensile strength on slope stability. Results show that the consideration of tension leads to a more conservative safety factor and a sharper curvature of the failure surface, and these impacts tend to be more obvious with the increases in slope inclination and slope width. Finally, the stability of the HB rock slope under seepage conditions is studied using the proposed approach. The results indicate that the effect of tensile strength is highly remarkable in seepage circumstances.

Efficient elimination and detection of phenolic compounds in juice using laccase mimicking nanozymes

Residual phenols in the juice can cause turbidity and affect its sensory quality.Laccase is used to remove phenolic compounds from fruit juice s.In order to overcome the shortcomings of natural laccase instability and high cost,in this work,we prepared a laccase mimic enzyme based on copper ion and adenosine monophosphate(AMP-Cu nanozymes).At the same mass concentration(1 mg·ml^(-1)), the catalytic activity of the nanozyme is about 15 times that of laccase.The AMP-Cu nanozymes had a higher V_(max) and a lower Km than laccase.The laccase mimic enzyme had a good stability under the condition of 30-90 ℃ and pH> 6.It also maintained high catalytic activity at high salt concentrations and 9 days storage time.Furthermore,the AMP-Cu nanozyme s maintained an initial catalytic activity of about 80% after six consecutive cycles of reaction.The linear range of detection of phenolic compounds by AMP-Cu nanozymes was 0.1-100 μmol·L^(-1) with a detection limit of 0.033 μmol·L^(-1).The phenol removal rate of AMP-Cu nanozymes was much higher than that of laccase under different reaction times.When the reaction was performed for 5 h,the phenol removal rate of the fruit juice by AMP-Cu nanozymes was about 65%.The efficient removal of phenolic compounds from different juices by AMP-Cu nanozymes indicate s that they have good application prospect in the food juice industry.

Comparative Analysis of the Complete Chloroplast Genome Sequences of Four Origin Plants of Lonicerae Flos(Lonicera;Caprifoliaceae)

Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the four origin plants are very similar in morphology,it is difficult to control the quality of LF in actual production.Over the past decade,many reports have pointed out the differences among them,including the botanical characteristics and active ingredients.However,there is still a lack of rapid methods that can be applied to the identification of the four origins.In this study,comparative analysis of the four chloroplast genomes was performed,and they showed low diversity(Pi=0.00267),three variation hotspots regions(rbcL-accD,rps12-ndhF and rps12-trnN-trnG)were identified as potentially molecular marker of highly informative.Meanwhile,the most obvious difference in SSR comparative analysis is reverse and complement repeats were only identified in L.confusa and L.hypoglauca,respectively.Lastly,the phylogenetic tree showed that L.confusa is more closely related to L.fulvotnetosa,while L.macranthoides is closer to L.hypoglauca.This study systematically revealed the differences among the four chloroplast genomes,and it provides valuable genetic information for identifying the origin of LF.

1,3-Dipolar Cycloaddition of Polycyclic Aromatic Azomethine Ylides and Alkynylbenziodoxoles for Synthesis of Functional Dibenzoullazines

A new family of dibenzoullazine derivatives was synthesized through 1,3-dipolar cycloaddition of polycyclic aromatic azomethine ylides with alkynylbenziodoxoles followed by oxidation.The benziodoxole moiety in the resulting products was used as a versatile linchpin for the synthesis of structurally diverse functional dibenzoullazines that are difficult to access by other synthetic methods.

Topology Optimization with Aperiodic Load Fatigue Constraints Based on Bidirectional Evolutionary Structural Optimization

Because of descriptive nonlinearity and computational inefficiency,topology optimization with fatigue life under aperiodic loads has developed slowly.A fatigue constraint topology optimization method based on bidirectional evolutionary structural optimization(BESO)under an aperiodic load is proposed in this paper.In viewof the severe nonlinearity of fatigue damagewith respect to design variables,effective stress cycles are extracted through transient dynamic analysis.Based on the Miner cumulative damage theory and life requirements,a fatigue constraint is first quantified and then transformed into a stress problem.Then,a normalized termination criterion is proposed by approximatemaximum stress measured by global stress using a P-normaggregation function.Finally,optimization examples show that the proposed algorithm can not only meet the requirements of fatigue life but also obtain a reasonable configuration.

Removal Effect of Nitrifying Bacteria on Ammonia Nitrogen in Water

[Objectives]To investigate the removal effect of nitrifying bacteria on ammonia nitrogen in water.[Methods]In this experiment,the treated water(referred to as raw water hereinafter)from the Changping Town Qiaoli Water Treatment Project in Dongguan City of Guangdong Province was used as the experimental water body,and the nitrifying bacteria liquid used in the project was taken as the experimental material,to explore the removal effect of the nitrifying bacteria liquid on the ammonia nitrogen in the water body.[Results]Under the condition that other variables remain unchanged,the more the amount of nitrifying bacteria liquid added,the higher the removal efficiency of nitrifying bacteria liquid;under the same conditions,the removal effect of ammonia nitrogen in a stirred water body is better than that in an unstirred water body;the removal effect of ammonia nitrogen in a water body with bio-media/carriers is better than that without bio-media/carriers.[Conclusions]Nitrifying bacteria have a better removal effect on the ammonia nitrogen in the water body.

Effect of cinnamaldehyde on Rhizopus stolonifer and on the conservation of sweet potato

Objectives:Rhizopus stolonifer,which causes soft rot of sweet potato,has resulted in substantial loss of economy postharvest.Materials and Methods:The antifungal effect and mechanism of cinnamaldehyde(CIN)against R.stolonifer were explored by biochemical analysis and RNA-sequencing in this research,and the edible quality of CIN-treated sweet potato was evaluated.Results:The results showed that CIN inhibited the growth of R.stolonifer and reduced the incidence of soft rot in sweet potato at a minimum inhibitory concentration of 1000μL/L.The damage of the cell walls of R.stolonifer by CIN was associated with the upregulation of CHT1.Cytosolic leakage and malondialdehyde content increased following CIN-treatment,which was correlated with increased reactive oxygen species levels and decreased catalase activity.Upregulation of ERG genes and oxidative stress-related genes following CIN treatment was associated with impaired cell membrane integrity.The mitochondrial structure of R.stolonifer was damaged by CIN treatment resulting in decreased respiration rates and ATP production,which was correlated with lower expression levels of IDH1,COX4,and QCR7.Conclusions:Our research suggests that the inhibition of CIN on R.stolonifer was related to the disruption of its normal gene expression network,and CIN maintained the nutritional and edible quality of sweet potato.This study provides valuable insights into the antifungal mechanism of CIN on R.stolonifer and the maintenance of root quality,which contributes to the effcient use of CIN for controlling soft rot in sweet potato.

陆相中低熟页岩油富集与原位转化科学问题及关键技术

围绕第281期双清论坛主题,本文回顾了陆相中低熟页岩油富集与原位转化研究现状,从陆相页岩油概念与类型、富有机质页岩形成机理、原位转化反应与传热机制、原位转化流动机制与原位开发技术五方面总结归纳了近年来的主要研究进展。从陆相有机质超量富集的环境响应与地质模型、陆相有机质超富段母质结构、能量场与产出物构成和固、液、气相有机质多相态、多场耦合流动机理三个方面归纳了关键科学问题与技术需求,并提出了五方面研究面临的难点和挑战,梳理了未来研究重点方向和国家自然科学基金资助的目标。

6,6’-Bieckol induces apoptosis and suppresses TGF-β-induced epithelial-mesenchymal transition in non-small lung cancer cells

Objective:In this study,the aim was to investigate the inhibitory effect of 6,6’-bieckol on the migration and epithelial-mesenchymal transition(EMT)of non-small cell lung cancer(NSCLC)cells,and explore its potential molecular mechanisms.Methods:Cell migration was measured using a CCK8,wound healing,and transwell migration assay.Apoptosis was determined using an Annexin V/propidium iodide staining.Western blotting and immunofluorescence were used to examine the expression level of apoptosis-related proteins and EMT marker proteins.Results:The results showed that 6,6’-bieckol inhibited migration and induced apoptosis of NSCLC cells.Furthermore,6,6’-bieckol had significantly up-regulated the E-cadherin and down-regulated Snail1 and Twist1 transcriptional levels.6,6’-Bieckol might inhibit TGF-β-induced EMT by down-regulating Snail1 and Twist1 and up-regulating E-cadherin in lung cancer cells.Conclusion:It is suggested that 6,6’-bieckol has the potential to be developed as a therapeutic candidate for lung cancer.

Assessment of the distribution and volume of air chambers around the inner auditory canal on high-resolution computed tomography scans of the temporal bone

To the Editor:Acoustic neuroma is the most common tumor in the cerebellopontine angle(CPA)area.The surgical approaches used for acoustic neuroma include the labyrinth,middle cranial fossa,posterior sigmoid sinus,and posterior labyrinth routes.However,regardless of the approach used to expose the tumor in the internal auditory canal(IAC),the bone around the IAC must be abraded,which inevitably exposes the surrounding air cells to damage and increases the risk of cerebrospinal fluid(CSF)leak after surgery.

荧光多肽探针靶向检测细胞和斑马鱼中的Cu^(2+)和S^(2-)

Cu^(2+)作为人体内含量最多的微量元素之一,在人正常的生理活动和新陈代谢中发挥着重要作用,而体内过量的Cu^(2+)则被发现与唐氏综合症、阿尔兹海默症等严重疾病密切相关.S^(2-)作为人体内广泛存在的阴离子,参与调控细胞内的氧化还原平衡、细胞凋亡、胰岛素分泌等各种生理过程,它的过度积累可能是阿尔兹海默症、帕金森的关键诱因.本文构建了一个Dansyl修饰的六肽荧光探针P(Dansyl-Asp-Glu-Pro-Gly-Ser-His),发现多肽探针P可以高特异性地识别Cu^(2+),而不受其他离子的干扰;它与Cu^(2+)以2:1的比例结合形成配合物2P-Cu,导致多肽探针的荧光淬灭.该配合物可以高选择性地检测S^(2-),S^(2-)的加入会置换出配合物中的Cu^(2+),从而恢复多肽探针的荧光.荧光实验表明,多肽探针P以"On-Off-On"的响应模式,实现对Cu^(2+)和S^(2-)的高灵敏检测,检测限分别为160和85 nM.并且,多肽探针P可成功用于活细胞和斑马鱼中Cu^(2+)和S^(2-)的成像.本文开发的新型荧光多肽探针具有生物相容性好、细胞毒性低等优点,可以用于细胞和活体中Cu^(2+)和S^(2-)的靶向检测,在Cu^(2+)和S^(2-)相关疾病的机理研究和诊断中具有广泛的应用潜力.

Regulatory Role of Retinoic Acid in Male Pregnancy of the Seahorse

Seahorses epitomize the exuberance of evolution.They have the unique characteristic of male pregnancy,which includes the carrying of many embryos in a brood pouch that incubates and nourishes the embryos,similar to the mammalian placenta.However,the regulatory networks underlying brood pouch formation and pregnancy remain largely unknown.In this study,comparative transcriptomic and metabolomic profiling on the lined seahorse Hippocampus erectus,with unformed,newly formed,and pregnant brood pouches identified a total of 141 and 2,533 differentially expressed genes together with 73 and 121 significantly differential metabolites related to brood pouch formation and pregnancy,respectively.Specifically,integrative omics analysis revealed that retinoic acid(RA)synthesis and signaling pathway played essential roles in the formation of the brood pouch and pregnancy.RA might function upstream of testosterone and progesterone,thereby directly influencing brood pouch formation by regulating the expression of fshr and cyp7a1.Our results also revealed that RA regulates antioxidant defenses,particularly during male pregnancy.Alternatively,pregnancy caused a consistent decrease in RA,canthaxanthin,astaxanthin,and glutathione synthetase,and an increase in susceptibility to oxidative stress,which may balance brood pouch development and reproduction in seahorses and pave the way to successful gestation.

Prognostic nomograms for young breast cancer:A retrospective study based on the SEER and METABRIC databases

Background:Young breast cancer(YBC)is a subset of breast cancer that is often more aggressive,but less is known about its prognosis.In this study,we aimed to generate nomograms to predict the overall survival(OS)and breast cancer‐specific survival(BCSS)of YBC patients.Methods:Data of women diagnosed with YBC between 2010 and 2020 were obtained from the Surveillance,Epidemiology,and End Results(SEER)database.The patients were randomly allocated into a training cohort(n=15,227)and internal validation cohort(n=6,526)at a 7:3 ratio.With the Cox regression models,significant prognostic factors were identified and used to construct 3‐,5‐,and 10‐year nomograms of OS and BCSS.Data from the Molecular Taxonomy of Breast Cancer International Consortium(METABRIC)database were used as an external validation cohort(n=90).Results:We constructed nomograms incorporating 10 prognostic factors for OS and BCSS.These nomograms demonstrated strong predictive accuracy for OS and BCSS in the training cohort,with C‐indexes of 0.806 and 0.813,respectively.The calibration curves verified that the nomograms have good prediction accuracy.Decision curve analysis demonstrated their practical clinical value for predicting YBC patient survival rates.Additionally,we provided dynamic nomograms to improve the operability of the results.The risk stratification ability assessment also showed that the OS and BCSS rates of the low‐risk group were significantly better than those of the high‐risk group.Conclusions:Here,we generated and validated more comprehensive and accurate OS and BCSS nomograms than models previously developed for YBC.These nomograms can help clinicians evaluate patient prognosis and make clinical decisions.