Genetic control of rhizosphere microbiome of the cotton plants under field conditions.

Understanding the extent of heritability of a plant-associated microbiome (phytobiome) is critically important for exploitation of phytobiomes in agriculture. Two crosses were made between pairs of cotton cultivars (Z2 and J11, L1 and Z49) with differential resistance to Verticillium wilt. F2 plants were grown in a field, together with the four parents to study the heritability of cotton rhizosphere microbiome. Amplicon sequencing was used to profile bacterial and fungal communities in the rhizosphere. F2 offspring plants of both crosses had higher average alpha diversity indices than the two parents; parents differed significantly from F2 offspring in Bray-Curtis beta diversity indices as well. Two types of data were used to study the heritability of rhizosphere microbiome: principal components (PCs) and individual top microbial operational taxonomic units (OTUs). For the L1 × Z49 cross, the variance among the F2 progeny genotypes (namely, genetic variance, VT) was significantly greater than the random variability (VE) for 12 and 34 out of top 100 fungal and bacterial PCs, respectively. For the Z2 × J11 cross, the corresponding values were 10 and 20 PCs. For 29 fungal OTUs and 10 bacterial OTUs out of the most abundant 100 OTUs, genetic variance (VT) was significantly greater than VE for the L1 × Z49 cross; the corresponding values for the Z2 × J11 cross were 24 and one. The estimated heritability was mostly in the range of 40% to 60%. These results suggested the existence of genetic control of polygenic nature for specific components of rhizosphere microbiome in cotton. KEY POINTS: • F2 offspring cotton plants differed significantly from parents in rhizosphere microbial diversity. • Specific rhizosphere components are likely to be genetically controlled by plants. • Common PCs and specific microbial groups are significant genetic components between the two crosses.

Fusarium pseudograminearum biomass and toxin accumulation in wheat tissues with and without Fusarium crown rot symptoms.

Fusarium crown rot (FCR) is an important and devastating disease of wheat (Triticum aestivum) caused by the fungus Fusarium pseudograminearum and related pathogens. Using two distinct susceptible cultivars, we investigated the isolation frequencies of F. pseudograminearum and quantified its biomass accumulation and the levels of the associated toxins deoxynivalenol (DON) and DON-3-glucoside (D3G) in inoculated field-grown wheat plants. We detected F. pseudograminearum in stem, peduncle, rachis, and husk tissues, but not in grains, whereas DON and D3G accumulated in stem, rachis, husk, and grain tissues. Disease severity was positively correlated with the frequency of pathogen isolation, F. pseudograminearum biomass, and mycotoxin levels. The amount of F. pseudograminearum biomass and mycotoxin contents in asymptomatic tissue of diseased plants were associated with the distance of the tissue from the diseased internode and the disease severity of the plant. Thus, apparently healthy tissue may harbor F. pseudograminearum and contain associated mycotoxins. This research helps clarify the relationship between F. pseudograminearum occurrence, F. pseudograminearum biomass, and mycotoxin accumulation in tissues of susceptible wheat cultivars with or without disease symptoms, providing information that can lead to more effective control measures.

Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air.

Raspberry production is under threat from the emerging fungal pathogenic genus Cladosporium. We used amplicon-sequencing, coupled with qPCR, to investigate how fruit age, fruit location within a polytunnel, polytunnel location and sampling date affected the fruit epiphytic microbiome. Fruit age was the most important factor impacting the fungal microbiome, followed by sampling date and polytunnel location. In contrast, polytunnel location and fruit age were important factors impacting the bacterial microbiome composition, followed by the sampling date. The within-tunnel location had a small significant effect on the fungal microbiome and no effect on the bacterial microbiome. As fruit ripened, fungal diversity increased and the bacterial diversity decreased. Cladosporium was the most abundant fungus of the fruit epiphytic microbiome, accounting for nearly 44% of all fungal sequences. Rotorod air samplers were used to study how the concentration of airborne Cladosporium inoculum (quantified by qPCR) varied between location (inside and outside the polytunnel) and time (daytime vs. nighttime). Quantified Cladosporium DNA was significantly higher during the day than the night and inside the polytunnel than the outside. This study demonstrated the dynamic nature of epiphytic raspberry fruit microbiomes and airborne Cladosporium inoculum within polytunnels, which will impact disease risks on raspberry fruit.

Lower serum uric acid and impairment of right cerebral hemisphere structural brain networks are related to depressive symptoms in cerebral small vessel disease: A cross-sectional study.

Cerebral small vessel disease (SVD) may be associated with an increased risk of depressive symptoms. Serum uric acid (SUA), an antioxidant, may be involved in the occurrence and development of depressive symptoms, but the mechanism remains unknown. Moreover, the relationship between structural brain networks and SUA has not been explored. This study examined the relationship between SUA and depressive symptoms in patients with SVD using graph theory analysis. We recruited 208 SVD inpatients and collected fasting blood samples upon admission. Depressive symptoms were assessed using the 24-item Hamilton Depression Rating Scale (HAMD-24). Magnetic resonance imaging was used to evaluate SVD, and diffusion tensor images were used to analyze structural brain networks using graph theory. Patients with depressive symptoms (n = 34, 25.76%) compared to those without (334.53 vs 381.28 µmol/L, p = 0.017) had lower SUA levels. Graph theoretical analyses showed a positive association of SUA with betweenness centrality, nodal efficiency, and clustering coefficients and a negative correlation with the shortest path length in SVD with depressive symptoms group. HAMD scores were significantly associated with nodal network metrics in the right cerebral hemisphere. Our findings suggested that lower SUA levels are significantly associated with disrupted structural brain networks in the right cerebral hemisphere of patients with SVD who have depressive symptoms.

Cerebral Perfusion Characteristics and Dynamic Brain Structural Changes in Stroke-Prone Renovascular Hypertensive Rats: A Preclinical Model for Cerebral Small Vessel Disease.

Hypertension is a leading cause of cerebral small vessel disease (CSVD) and vascular dementia in elderly individuals. We aimed to assess cerebral perfusion and dynamic changes in brain structure in stroke-prone renovascular hypertensive rats (RHRSPs) with different durations of hypertension and to investigate whether they have pathophysiological features similar to those of humans with CSVD. The RHRSP model was established using the two-kidney, two-clip (2k2c) method, and the Morris water maze (MWM) test, MRI, immunohistochemistry, and biochemical analysis were performed at multiple time points for up to six months following the 2k2c operation. Systolic blood pressure was significantly greater in the RHRSP group than in the sham-operated group at week 4 post-surgery and continued to increase over time, leading to cognitive decline by week 20. Arterial spin labeling revealed cerebral hypoperfusion in the RHRSP group at 8 weeks, accompanied by vascular remodeling and decreased vessel density. Diffusion tensor imaging and Luxol fast blue staining indicated that white matter disintegration and demyelination gradually progressed in the corpus callosum and that myelin basic protein levels decreased. Eight weeks after surgery, blood-brain barrier (BBB) leakage into the corpus callosum was observed. The albumin leakage area was negatively correlated with the myelin sheath area (r=-0.88, p<0.001). RNA-seq analysis revealed downregulation of most angiogenic genes and upregulation of antiangiogenic genes in the corpus callosum of RHRSPs 24 weeks after surgery. RHRSPs developed cerebral hypoperfusion, BBB disruption, spontaneous white matter damage, and cognitive impairment as the duration of hypertension increased. RHRSPs share behavioral and neuropathological characteristics with CSVD patients, making them suitable animal models for preclinical trials related to CSVD.

Nonlinear dynamics of cavity optomechanical-thermal systems.

Cavity optomechanics is concerned with the interaction between optical cavities and mechanical resonators. Here, we present systematic research on the dynamic behaviors of cavity optomechanical systems incorporating the influence of thermal nonlinearity. A dimensionless theoretical model was established to describe the system and numerical simulations were performed to study the dynamic behaviors. We theoretically identify the staircase effect, which can abruptly alter the system parameters when adiabatically sweeping the pump laser frequency across the optical cavity resonance and driving the mechanical resonator into oscillation. Moreover, we found bistability effects in several detuning intervals when sweeping the laser forward and backward. Both effects are analyzed theoretically and the roots lie in the thermal instability between averaged cavity energy and laser detuning. Our study shows the dynamic behaviors in an optomechanical-thermal system and provides guidance in leveraging the systems for applications in optical frequency comb, phonon laser, etc.

The secreted feruloyl esterase of Verticillium dahliae modulates host immunity via degradation of GhDFR.

Feruloyl esterase (ferulic acid esterase, FAE) is an essential component of many biological processes in both eukaryotes and prokaryotes. This research aimed to investigate the role of FAE and its regulation mechanism in plant immunity. We identified a secreted feruloyl esterase VdFAE from the hemibiotrophic plant pathogen Verticillium dahliae. VdFAE acted as an important virulence factor during V. dahliae infection, and triggered plant defence responses, including cell death in Nicotiana benthamiana. Deletion of VdFAE led to a decrease in the degradation of ethyl ferulate. VdFAE interacted with Gossypium hirsutum protein dihydroflavanol 4-reductase (GhDFR), a positive regulator in plant innate immunity, and promoted the degradation of GhDFR. Furthermore, silencing of GhDFR led to reduced resistance of cotton plants against V. dahliae. The results suggested a fungal virulence strategy in which a fungal pathogen secretes FAE to interact with host DFR and interfere with plant immunity, thereby promoting infection.

Dynamics of Puccinia striiformis f. sp. tritici Urediniospores and Its Relationship with Meteorological Factors in Mianyang, China.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the main diseases of wheat worldwide. Mianyang of Sichuan province in Southwest China is one of main regions for winter Pst inoculum production and spring epidemic and provides urediniospores for infecting wheat in the surrounding regions. Understanding the urediniospore dynamics is important to predict and manage stripe rust. In this study, spore trapping coupled with a TaqMan real-time quantitative PCR method was used to monitor airborne Pst urediniospores from December 2019 to December 2022 in Mianyang. Weather conditions (temperature, relative humidity, daily sunshine duration, and precipitation) were collected for the same period. These data were used to study the relationship of airborne urediniospore density with climatic conditions. The results showed that Pst urediniospores were captured all year round, and the annual peak of urediniospore densities occurred in the period from March to April in which the urediniospores accounted for the largest proportion of the annual total urediniospores. The density of urediniospores in the period of March to April was linearly related to the average sunshine duration of 20 days and average temperature of 15 days prior to the final day of a 7-day trapping period. This relationship needs to be tested in other regions where Pst can sporulate during the winter before it can be integrated with Pst infection conditions to predict rust development.

Population Genetic Structure of the Rubber Tree Powdery Mildew Pathogen (Erysiphe quercicola) from China.

In order to manage agricultural pathogens, it is crucial to understand the population structure underlying epidemics. Rubber tree powdery mildew, caused by Erysiphe quercicola, is a serious threat to rubber plantations worldwide, especially in subtropical environments including all rubber tree-growing regions in China. However, the population structure of the pathogen is uncertain. In this study, 16 polymorphic microsatellite markers were used to genotype powdery mildew samples from the main rubber tree-growing regions including Yunnan (YN), Hainan (HN), western Guangdong (WG), and eastern Guangdong (EG). YN had higher genotypic diversity (Simpson's indices), genotypic evenness, Nei's gene diversity, allelic richness, and private allelic richness than the other regions. Cluster analysis, discriminant analysis of principal components, pairwise divergence, and shared multilocus genotype analyses all showed that YN differed significantly from the other regions. The genetic differentiation was small among the other three regions (HN, WG, and EG). Analysis of molecular variance indicated that the variability among regions accounted for 22.37% of the total variability. Genetic differentiation was significantly positively correlated (Rxy = 0.772, P = 0.001) with geographic distance. Linkage equilibrium analysis suggested possible occurrence of sexual recombination although asexual reproduction predominates in E. quercicola. The results suggested that although significant genetic differentiation of E. quercicola occurred between YN and the other regions, pathogen populations from the other three regions lacked genetic differentiation.

Anisotropic Superconducting Nb2 CTx MXene Processed by Atomic Exchange at the Wafer Scale.

Superconductivty has recently been induced in MXenes through surface modification. However, the previous reports have mostly been based on powders or cold-pressed pellets, with no known reports on the intrinsic superconsucting properties of MXenes at the nanoale. Here, it is developed a high-temperature atomic exchange process in NH3 atmosphere which induces superconductivity in either singleflakes or thin films of Nb2 CTx MXene. The exchange process between nitrogen atoms and fluorine, carbon, and oxygen atoms in the MXene lattice and related structural adjustments are studied using both experiments and density functional theory. Using either single-flake or thin-film devices, an anisotropic magnetic response of the 2D superconducting transformation has been successfully revealed. The anisotropic superconductivity is further demonstrated using superconducting thin films uniformly deposited over a 4 in. wafers, which opens up the possibility of scalable MXene-based superconducting devices.

Development of a whole-slide-level segmentation-based dMMR/pMMR deep learning detector for colorectal cancer.

To investigate whole-slide-level prediction in the field of artificial intelligence identification of dMMR/pMMR from hematoxylin and eosin (H&E) in colorectal cancer (CRC), we established a segmentation-based dMMR/pMMR deep learning detector (SPEED). Our model was approximately 1,700 times faster than that of the classification-based model. For the internal validation cohort, our model yielded an overall AUC of 0.989. For the external validation cohort, the model exhibited a high performance, with an AUC of 0.865. The human‒machine strategy further improved the model performance for external validation by an AUC up to 0.988. Our whole-slide-level prediction model provided an approach for dMMR/pMMR detection from H&E whole slide images with excellent predictive performance and less computer processing time in patients with CRC.

Subnoise optical covert communication based on amplified spontaneous emission light.

Amplified spontaneous emission (ASE) light is a common noise in optical communication systems with optical amplification, and a suitable optical carrier for optical covert communication. To deeply covert the secure signal, an in-band subnoise optical covert communication scheme is proposed and demonstrated by a proof-of-concept experiment. The power spectral density of optical secure channel is 10 dB less than the optical noise in the public channel. The covert signal is hidden in both optical and electrical domain, and can be transmitted with error-free. The trade-off between covertness and availability is discussed.

Dose-Dependent Genetic Resistance to Azole Fungicides Found in the Apple Scab Pathogen.

The evolution of azole resistance in fungal pathogens presents a major challenge in both crop production and human health. Apple orchards across the world are faced with the emergence of azole fungicide resistance in the apple scab pathogen Venturia inaequalis. Target site point mutations observed in this fungus to date cannot fully explain the reduction in sensitivity to azole fungicides. Here, polygenic resistance to tebuconazole was studied across a population of V. inaequalis. Genotyping by sequencing allowed Quantitative Trait Loci (QTLs) mapping to identify the genetic components controlling this fungicide resistance. Dose-dependent genetic resistance was identified, with distinct genetic components contributing to fungicide resistance at different exposure levels. A QTL within linkage group seven explained 65% of the variation in the effective dose required to reduce growth by 50% (ED50). This locus was also involved in resistance at lower fungicide doses (ED10). A second QTL in linkage group one was associated with dose-dependent resistance, explaining 34% of variation at low fungicide doses (ED10), but did not contribute to resistance at higher doses (ED50 and ED90). Within QTL regions, non-synonymous mutations were observed in several ATP-Binding Cassette and Major Facilitator SuperFamily transporter genes. These findings provide insight into the mechanisms of fungicide resistance that have evolved in horticultural pathogens. Identification of resistance gene candidates supports the development of molecular diagnostics to inform management practices.

A novel gain-of-function PIP4K2A mutation elevates the expression of ß-globin and aggravates the severity of α-thalassemia.

Haemoglobin H (Hb H) disease (intermediate status of α-thalassemia) shows marked phenotypic variability from asymptomatic to severe anaemia. Apart from the combined ß-thalassemia allele ameliorating clinical severity, reports of genetic modifier genes affecting the phenotype of Hb H disease are scarce which bring inconvenience to precise diagnosis and genetic counselling of the patients. Here, we present a novel mutation (c.948C>A, p.S316R) in the PIP4K2A gene in a female Hb H disease patient who displayed moderate anaemia and a relatively high Hb H level. Haematological analysis in her family members revealed that individuals carrying this mutation have upregulated ß-globin expression, leading to a more imbalanced ß/α-globin ratio and more Hb H inclusion bodies in peripheral red blood cells. According to functional experiments, the mutant PIP4K2A protein exhibits enhanced protein stability, increased kinase activity and a stronger regulatory effect on downstream proteins, suggesting a gain-of-function mutation. Moreover, introduction of the S316R mutation into HUDEP-2 cells increased expression of ß-globin, further inhibiting erythroid differentiation and terminal enucleation. Thus, the S316R mutation is a novel genetic factor associated with ß-globin expression, and the PIP4K2A gene is a new potential modifier gene affecting the α-thalassemia phenotype.

Hydrothermal preparation of NiO/La-NaTaO3 composite photocatalyst for degradation of ammonium dibutyl dithiophosphate wastewater.

The discharge of a large amount of flotation reagents wastewater can cause significant environmental pollution. In this study, NiO/La-NaTaO3 nano-photocatalyst was prepared and applied to degrade synthetic flotation reagent ammonium dibutyl dithiophosphate wastewater. Various characterization results confirmed the successful synthesis of NiO/La-NaTaO3, and UV-vis DRS analysis revealed a band gap of 3.96 eV for 4 wt% NiO/2.5% La-NaTaO3. Under UV light, the degradation rate of 20 mg 4 wt% NiO/2.5% La-NaTaO3 photocatalyst reached its optimum within 4.5 h at pH=3, exhibiting a 1.45 times improvement compared to pure NaTaO3. Radical trapping experiments and EPR results showed that ·OH and·O2- showed major contribution to the degradation. Furthermore, photocatalytic mechanisms and toxicity evolution were investigated, demonstrating the potential application of photocatalytic methods for treating flotation reagent wastewater.

Integrated microbiology and metabolomics analysis reveal responses of cotton rhizosphere microbiome and metabolite spectrum to conventional seed coating agents.

Fludioxonil (FL) and metalaxyl-M·fludioxonil·azoxystrobin (MFA) are conventional seed coating agents for controlling cotton seedling diseases. However, their effects on seed endophytic and rhizosphere microecology are still poorly understood. This study aimed to assess the effects of FL and MFA on cotton seed endophytes, rhizosphere soil enzymatic activities, microbiome and metabolites. Both seed coating agents significantly changed seed endophytic bacterial and fungal communities. Growing coated seeds in the soils originating from the Alar (AL) and Shihezi (SH) region inhibited soil catalase activity and decreased both bacterial and fungal biomass. Seed coating agents increased rhizosphere bacterial alpha diversity for the first 21 days but decreased fungal alpha diversity after day 21 in the AL soil. Seed coating reduced the abundance of a number of beneficial microorganisms but enriched some potential pollutant-degrading microorganisms. Seed coating agents may have affected the complexity of the co-occurrence network of the microbiome in the AL soil, reducing connectivity, opposite to what was observed in the SH soil. MFA had more pronounced effects on soil metabolic activities than FL. Furthermore, there were strong links between soil microbial communities, metabolites and enzymatic activities. These findings provide valuable information for future research and development on application of seed coatings for disease management.

TAK1 Improves Cognitive Function via Suppressing RIPK1-Driven Neuronal Apoptosis and Necroptosis in Rats with Chronic Hypertension.

Chronic hypertension is a major risk factor for cognitive impairment, which can promote neuroinflammation and neuronal loss in the central nervous system. Transforming growth factor ß-activated kinase 1 (TAK1) is a key molecular component in determining cell fate and can be activated by inflammatory cytokines. This study aimed to investigate the role of TAK1 in mediating neuronal survival in the cerebral cortex and hippocampus under chronic hypertensive conditions. To that end, we used stroke-prone renovascular hypertension rats (RHRSP) as chronic hypertension models. Adeno-associated virus (AAV) designed to overexpress or knock down TAK1 expression were injected into the lateral ventricles of rats and the subsequent effects on cognitive function and neuronal survival under chronic hypertensive conditions were assessed. We found that, TAK1 knockdown in RHRSP markedly increased neuronal apoptosis and necroptosis and induced cognitive impairment, which could be reversed by Nec-1s, an inhibitor of receptor interacting protein kinase 1 (RIPK1). In contrast, overexpression of TAK1 in RHRSP significantly suppressed neuronal apoptosis and necroptosis and improved cognitive function. Further knockdown of TAK1 in sham-operated rats received similar phenotype with RHRSP. The results have been verified in vitro. In this study, we provide in vivo and in vitro evidence that TAK1 improves cognitive function by suppressing RIPK1-driven neuronal apoptosis and necroptosis in rats with chronic hypertension.

Dynamics of Puccinia striiformis f. sp. tritici Urediniospores in Longnan, a Critical Oversummering Region of China.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici Erikss. (Pst), is a devastating disease resulting in yield reduction. Because the temperature limits the overwintering and oversummering of Pst, it cannot complete the whole year cycle in most areas of China. Longnan, located in the southeast of Gansu Province, is one of the annual cycle areas of Pst, which can supply urediniospores in autumn to eastern wheat-growing areas in China. In this study, a TaqMan real-time quantitative PCR (TaqMan-qPCR) detection system for Pst urediniospores was established, and the detection limit was a single urediniospore. The dynamics of Pst urediniospores in Longnan were monitored by spore trapping and TaqMan-qPCR for 3 years. Meanwhile, the meteorological conditions including air temperature, relative humidity, and precipitation were recorded. Results showed that Pst urediniospores can be captured from March to December, and two peaks of urediniospore density appeared in May and June, respectively. The density of urediniospore is closely related to temperature and precipitation from March to June. In addition, we found that the density of Pst urediniospore had the peak value when the average air temperature was 10 to 21°C, and the relative humidity was 60 to 85% from May to June. The exponential model could describe the variation of Pst urediniospore density based on average temperature and precipitation from March to June. It is worth mentioning that the exponential model based on average temperature 7 days before spore capture has a great advantage in predicting the urediniospore density in the air. This study laid a foundation for establishment of a prediction model for wheat stripe rust based on the density of urediniospores and meteorological factors.

Gradient torque and its effect on rotational dynamics of optically trapped non-spherical particles in the elliptic Gaussian beam.

Rotational motion of the optically trapped particle is a topic of enduring interest, while the changes of angular velocity in one rotation period remain largely unexplored. Here, we proposed the optical gradient torque in the elliptic Gaussian beam, and the instantaneous angular velocities of alignment and fluctuant rotation of the trapped non-spherical particles are investigated for the first time. The fluctuant rotations of optically trapped particles are observed, and the angular velocity fluctuated twice per rotation period, which can be used to determine the shape of trapped particles. Meanwhile, a compact optical wrench is invented based on the alignment, and its torque is adjustable and is larger than the torque of a linearly polarized wrench with the same power. These results provide a foundation for precisely modelling the rotational dynamics of optically trapped particles, and the presented wrench is expected to be a simple and practical micro-manipulating tool.

Quantitative trait loci associated with apple endophytes during pathogen infection.

The plant phyllosphere is colonized by microbial communities that can influence the fitness and growth of their host, including the host's resilience to plant pathogens.There are multiple factors involved in shaping the assemblages of bacterial and fungal endophytes within the phyllosphere, including host genetics and environment. In this work, the role of host genetics in plant-microbiome assembly was studied in a full-sibling family of apple (Malus x domestica) trees infected with the fungal pathogen Neonectria ditissima. A Quantitative Trait Loci (QTL) analysis showed that there are multiple loci which influence the abundance of individual endophytic taxa, with the majority of QTL having a moderate to large effect (20-40%) on endophyte abundance. QTL regions on LG 1, 3, 4, 5, 10, 12, 13, 14 and 15 were shown to affect multiple taxa. Only a small proportion of the variation in overall taxonomic composition was affected by host genotype, with significant QTL hits for principal components explaining <8% and <7.4% of the total variance in bacterial and fungal composition, respectively. Four of the identified QTL colocalised with previously identified regions associated with tolerance to Neonectria ditissima. These results suggest that there is a genetic basis shaping apple endophyte composition and that microbe-host associations in apple could be tailored through breeding.