Effects of sleep on the glymphatic functioning and multimodal human brain network affecting memory in older adults.

Understanding how sleep affects the glymphatic system and human brain networks is crucial for elucidating the neurophysiological mechanism underpinning aging-related memory declines. We analyzed a multimodal dataset collected through magnetic resonance imaging (MRI) and polysomnographic recording from 72 older adults. A proxy of the glymphatic functioning was obtained from the Diffusion Tensor Image Analysis along the Perivascular Space (DTI-ALPS) index. Structural and functional brain networks were constructed based on MRI data, and coupling between the two networks (SC-FC coupling) was also calculated. Correlation analyses revealed that DTI-ALPS was negatively correlated with sleep quality measures [e.g., Pittsburgh Sleep Quality Index (PSQI) and apnea-hypopnea index]. Regarding human brain networks, DTI-ALPS was associated with the strength of both functional connectivity (FC) and structural connectivity (SC) involving regions such as the middle temporal gyrus and parahippocampal gyrus, as well as with the SC-FC coupling of rich-club connections. Furthermore, we found that DTI-ALPS positively mediated the association between sleep quality and rich-club SC-FC coupling. The rich-club SC-FC coupling further mediated the association between DTI-ALPS and memory function in good sleepers but not in poor sleepers. The results suggest a disrupted glymphatic-brain relationship in poor sleepers, which underlies memory decline. Our findings add important evidence that sleep quality affects cognitive health through the underlying neural relationships and the interplay between the glymphatic system and multimodal brain networks.

Construction of an ER stress-related prognostic signature for predicting prognosis and screening the effective anti-tumor drug in osteosarcoma.

BACKGROUND: Osteosarcoma is the most common malignant primary bone tumor in infants and adolescents. The lack of understanding of the molecular mechanisms underlying osteosarcoma progression and metastasis has contributed to a plateau in the development of current therapies. Endoplasmic reticulum (ER) stress has emerged as a significant contributor to the malignant progression of tumors, but its potential regulatory mechanisms in osteosarcoma progression remain unknown. METHODS: In this study, we collected RNA sequencing and clinical data of osteosarcoma from The TCGA, GSE21257, and GSE33382 cohorts. Differentially expressed analysis and the least absolute shrinkage and selection operator regression analysis were conducted to identify prognostic genes and construct an ER stress-related prognostic signature (ERSRPS). Survival analysis and time dependent ROC analysis were performed to evaluate the predictive performance of the constructed prognostic signature. The "ESTIMATE" package and ssGSEA algorithm were utilized to evaluate the differences in immune cells infiltration between the groups. Cell-based assays, including CCK-8, colony formation, and transwell assays and co-culture system were performed to assess the effects of the target gene and small molecular drug in osteosarcoma. Animal models were employed to assess the anti-osteosarcoma effects of small molecular drug. RESULTS: Five genes (BLC2, MAGEA3, MAP3K5, STC2, TXNDC12) were identified to construct an ERSRPS. The ER stress-related gene Stanniocalcin 2 (STC2) was identified as a risk gene in this signature. Additionally, STC2 knockdown significantly inhibited osteosarcoma cell proliferation, migration, and invasion. Furthermore, the ER stress-related gene STC2 was found to downregulate the expression of MHC-I molecules in osteosarcoma cells, and mediate immune responses through influencing the infiltration and modulating the function of CD8+ T cells. Patients categorized by risk scores showed distinct immune status, and immunotherapy response. ISOX was subsequently identified and validated as an effective anti-osteosarcoma drug through a combination of CMap database screening and in vitro and in vivo experiments. CONCLUSION: The ERSRPS may guide personalized treatment decisions for osteosarcoma, and ISOX holds promise for repurposing in osteosarcoma treatment.

Antibiotic feeding changes the bacterial community of Chilo suppressalis and thereby affects its pesticide tolerance.

BACKGROUND: Owing to the widespread use of chemical pesticides to control agricultural pests, pesticide tolerance has become a serious problem. In recent years, it has been found that symbiotic bacteria are related to pesticides tolerance. To investigate the potential role of microorganisms in the pesticide tolerance of Chilo suppressalis, this study was conducted. RESULTS: The insect was fed with tetracycline and cefixime as the treatment group (TET and CFM, respectively), and did not add antibiotics in the control groups (CK). The 16S rDNA sequencing results showed that antibiotics reduced the diversity of C. suppressalis symbiotic microorganisms but did not affect their growth and development. In bioassays of the three C. suppressalis groups (TET, CFM, and CK), a 72 h LC50 fitting curve was calculated to determine whether long-term antibiotic feeding leads to a decrease in pesticide resistance. The CK group of C. suppressalis was used to determine the direct effect of antibiotics on pesticide tolerance using a mixture of antibiotics and pesticides. Indirect evidence suggests that antibiotics themselves did not affect the pesticide tolerance of C. suppressalis. The results confirmed that feeding C. suppressalis cefixime led to a decrease in the expression of potential tolerance genes to chlorantraniliprole. CONCLUSIONS: This study reveals the impact of antibiotic induced changes in symbiotic microorganisms on the pesticide tolerance of C. suppressalis, laying the foundation for studying the interaction between C. suppressalis and microorganisms, and also providing new ideas for the prevention and control of C. suppressalis and the creation of new pesticides.

Defence and nutrition synergistically contribute to the distinct tolerance of rice subspecies to the stem borer, Chilo suppressalis.

Damage caused by the rice striped stem borer (SSB), Chilo suppressalis (Walker) (Lepidoptera: Pyralidae), is much more severe on indica/xian rice than on japonica/geng rice (Oryza sativa) which matches pest outbreak data in cropping regions of China. The mechanistic basis of this difference among rice subspecies remains unclear. Using transcriptomic, metabolomic and genetic analyses in combination with insect bioassay experiments, we showed that japonica and indica rice utilise different defence responses to repel SSB, and that SSB exploited plant nutrition deficiencies in different ways in the subspecies. The more resistant japonica rice induced patterns of accumulation of methyl jasmonate (MeJA-part of a defensive pathway) and vitamin B1 (VB1-a nutrition pathway) distinct from indica cultivars. Using gene-edited rice plants and SSB bioassays, we found that MeJA and VB1 jointly affected the performance of SSB by disrupting juvenile hormone levels. In addition, genetic variants of key biosynthesis genes in the MeJA and VB1 pathways (OsJMT and OsTH1, respectively) differed between japonica and indica rice and contributed to performance differences; in indica rice, SSB avoided the MeJA defence pathway and hijacked the VB1 nutrition-related pathway to promote development. The findings highlight important genetic and mechanistic differences between rice subspecies affecting SSB damage which could be exploited in plant breeding for resistance.

Indirect Impact of Eutrophication on Occurrence, Air-Water Exchange, and Vertical Sinking Fluxes of Antibiotics in a Subtropical River.

A significant challenge that warrants attention is the influence of eutrophication on the biogeochemical cycle of emerging contaminants (ECs) in aquatic environments. Antibiotics pollution in the eutrophic Pearl River in South China was examined to offer new insights into the effects of eutrophication on the occurrence, air-water exchange fluxes (Fair-water), and vertical sinking fluxes (Fsinking) of antibiotics. Antibiotics transferred to the atmosphere primarily through aerosolization controlled by phytoplankton biomass and significant spatiotemporal variations were observed in the Fair-water of individual antibiotics throughout all sites and seasons. The Fsinking of ∑AB14 (defined as a summary of 14 antibiotics) was 750.46 ± 283.19, 242.71 ± 122.87, and 346.74 ± 249.52 ng of m-2 d-1 in spring, summer, and winter seasons. Eutrophication indirectly led to an elevated pH, which reduced seasonal Fair-water of antibiotics, sediment aromaticity, and phytoplankton hydrophobicity, thereby decreasing antibiotic accumulation in sediments and phytoplankton. Negative correlations were further found between Fsinking and the water column daily loss of antibiotics with phytoplankton biomass. The novelty of this study is to provide new complementary knowledge for the regulation mechanisms of antibiotics by phytoplankton biological pump, offering novel perspectives and approaches to understanding the coupling between eutrophication and migration and fate of antibiotics in a subtropical eutrophic river.

Cardiopulmonary Response to Acute Exercise before Hemodialysis: A Pilot Study.

INTRODUCTION: Disparities in physical fitness between immediately before dialysis (pre-D) and the day following dialysis (non-D) have not been investigated despite potential adverse factors such as fluid status, uremia, and electrolyte levels in the pre-dialysis period. The effect of acute exercise immediately before hemodialysis (HD) on HD-related hypotension remains unclear. We hypothesized that cardiopulmonary performance and muscular strength would be inferior in the immediate pre-D period compared to those non-D. METHODS: Twenty patients receiving chronic HD treatments underwent symptom-limited incremental cardiopulmonary exercise testing (CPET) and isokinetic testing both 1-2 h prior to dialysis (pre-D) and non-D. This investigation was a sub-study of a clinical trial assessing the efficacy of a pre-D exercise training program. Blood pressure profiles during HD post-CPET and pre-D exercise training were compared with those during usual HD sessions. RESULTS: No adverse events were observed during the 80 exercise tests. Prior to dialysis, the nadir of the ventilatory equivalent of CO2 was slightly elevated, the resting heart rate was lower, and the peak systolic blood pressure was higher than those non-D. Contrary to our hypothesis, peak V˙O2 and quadriceps peak torque showed no differences. Blood pressure profiles during HD post-exercise were similar to those during sessions without prior exercise, except for a lower resting systolic blood pressure at the beginning of HD. CONCLUSION: Cardiopulmonary response and muscular strength in the 1-2 h prior to HD were comparable with those on the day following HD, with only minor clinically insignificant differences. Acute exercise prior to HD did not affect the magnitude of hypotension during HD. This study suggests a potential alternative timing for exercise training or testing in patients undergoing chronic HD.

Development and validation of a nomogram-based model to predict combined esophageal injury post-esophagoscopy for esophageal foreign bodies.

OBJECTIVE: The aim of this study is to create and validate a nomogram model for predicting complications of esophageal injury post-esophagoscopy in patients with esophageal foreign bodies (EFB). METHODS: We examined 303 patients who underwent esophagoscopy from January 2019 to December 2022 at a leading hospital in Anhui, known for its expertise in otorhinolaryngology-head and neck surgery. The patients were split into a modeling group and a validation group in a 7:3 ratio. Logistic regression analysis was employed to determine the risk factors for esophageal injury after undergoing esophagoscopy in patients with EFB. Based on these factors, a nomogram risk prediction model was developed and assessed using a goodness of fit test. RESULTS: Logistic regression analysis revealed that the type of foreign body, failure of gastroscopic retrieval, duration of lodgment, lodgment site, and presence of combined cardiovascular and cerebrovascular diseases were significant (p < 0.05) independent risk factors for esophageal injury following esophagoscopy for EFB. The area under the ROC curve for the training set was 0.850, and the Hosmer-Lemeshow goodness of fit test resulted in a p value of 0.908. For the validation set, the area under the ROC curve was 0.848, and the Hosmer-Lemeshow test gave a p value of 0.665. The calibration curve showed a close alignment between the predicted and observed values. CONCLUSION: The type of foreign body, duration of lodgment, lodgment site, previous failure of gastroscopic retrieval, and history of combined cardiovascular and cerebrovascular diseases are significant risk factors for esophageal injury following EFB esophagoscopy. This model accurately quantifies the risk of esophageal injury after EFB esophagoscopy.

Efficacy of Lemon Mouthwash in Improving Dry Mouth Symptoms and Salivary Flow in Hemodialysis Patients.

OBJECTIVES: Gargling mouthwash is a safe and convenient oral care intervention; it rinses the mouth and increases salivary flow rate. The effectiveness of lemon mouthwash in relieving xerostomia and increasing the salivary flow rate among hemodialysis patients has not been studied. Our study sought to analyze the effectiveness of varying concentrations of lemon in mouthwash solutions on xerostomia and salivary flow rate. METHODS: A multi-concentration test was used to assess lemon mouthwash at 20%, 15%, 10%, 5%, and 2.5% concentrations to determine the optimal concentration for relieving dry mouth and increasing salivary flow rate. Generalized estimating equations were used to analyze the differences between various concentrations of lemon mouthwash and baseline values. RESULTS: In total, 44 patients were recruited. The 10% lemon concentration mouthwash was the most effective for increasing salivary flow rate, but the 5% and 2.5% were better accepted by the participants. Our findings can help establish intervention guidelines to relieve xerostomia among hemodialysis patients. CONCLUSION: Our findings can help establish intervention guidelines to relieve xerostomia among hemodialysis patients.

Tyrosine hydroxylase plays crucial roles in larval cuticle formation and larval-pupal tanning in the rice stem borer, Chilo suppressalis.

The striped stem borer, Chilo suppressalis (Walker), a notorious pest infesting rice, has evolved a high level of resistance to many commonly used insecticides. In this study, we investigate whether tyrosine hydroxylase (TH), which is required for larval development and cuticle tanning in many insects, could be a potential target for the control of C. suppressalis. We identified and characterized the full-length cDNA (CsTH) of C. suppressalis. The complete open reading frame of CsTH (MW690914) was 1683 bp in length, encoding a protein of 560 amino acids. Within the first to the sixth larval instars, CsTH was high in the first day just after molting, and lower in the ensuing days. From the wandering stage to the adult stage, levels of CSTH began to rise and reached a peak at the pupal stage. These patterns suggested a role for the gene in larval development and larval-pupal cuticle tanning. When we injected dsCsTH or 3-iodotyrosine (3-IT) as a TH inhibitor or fed a larva diet supplemented with 3-IT, there were significant impairments in larval development and larval-pupal cuticle tanning. Adult emergence was severely impaired, and most adults died. These results suggest that CsTH might play a critical role in larval development as well as larval-pupal tanning and immunity in C. suppressalis, and this gene could form a potential novel target for pest control.

The irregular developmental duration mainly caused by the broad-complex in Chilo suppressalis.

Chilo suppressalis, a critical rice stem borer pest, poses significant challenges to rice production due to its overlapping generations and irregular developmental duration. These characteristics complicate pest management strategies. According to the dynamic analysis of the overwintering adults of C. suppressalis in fields, it indicates that the phenomenon of irregular development of C. suppressalis exists widely and continuously. This study delves into the potential role of the Broad-Complex (Br-C) gene in the developmental duration of C. suppressalis. Four isoforms of Br-C, named CsBr-C Z1, CsBr-C Z2, CsBr-C Z4, and CsBr-C Z7, were identified. After CsBr-Cs RNAi, the duration of larva development spans extended obviously. And, the average developmental duration of dsCsBr-Cs feeding individuals increased obviously. Meanwhile, the average developmental duration of the dsCsBr-C Z2 feeding group was the longest among all the RNAi groups. After dsCsBr-Cs feeding continuously, individuals pupated at different instars changed obviously: the proportion of individuals pupated at the 5th instar decreased and pupated at the 7th instar or higher increased significantly. Moreover, the pupation rate of dsCsBr-Cs (except dsCsBr-C Z7) were significantly lower than that of dsGFP. The same results were obtained from the mutagenesis in CsBr-C genes mediated by CRISPR/Cas9. The average developmental duration of CsBr-Cs knockout individuals was significantly prolonged. And, the instar of pupation in knockout individuals was also delayed significantly. In conclusion, this work showed that CsBr-Cs played a crucial role in pupal commitment and affected the developmental duration of C. suppressalis significantly.

A simple and efficient method for selective recovery of copper from nitric acid leaching solution of printed circuit boards containing nickel, zinc, lead, aluminum, and iron.

The Cu content in discarded printed circuit boards (PCBs) is a crucial aspect, and employing suitable methods for the recovery of Cu holds significance in resource recovery. However, the selective recovery of Cu from an acidic leaching solution containing multiple metals such as Ni, Zn, and Pb poses challenges. L-cys contains the thiol (-SH), the amino (-NH2) and the carboxyl (-COOH) groups, which may complex with metal ions. In particular, the reaction between thiol groups and metal ions makes it possible to recover Cu. In this study, we propose an innovative method using L-cysteine (L-cys) to recover Cu from the acidic leaching solution of discarded PCBs. The effects of Ni2+, Zn2+, Pb2+, Al3+, and Fe3+ irons on the recovery of Cu were studied based on the concentration of these metal ions in PCBs. Adding 120 mL of 2 g/L solution of L-cys to 100 mL of 500 mg/L solution of Cu(NO3)2 achieved the complete recovery of Cu by forming precipitates. The Ni2+, Zn2+, Pb2+, and Al3+ ions did not affect the recovery of Cu within the studied metal concentration range in the acidic leaching solution. However, approximately 20% of the Fe3+ is coprecipitated during the recovery of Cu. This is mainly affected by the amount of colloid formed when copper precipitates in the solution. The interference of Fe3+ on copper recovery can be effectively reduced by controlling the volume of L-cys to reduce the formation of colloid. Fourier transform infrared and X-ray photoelectron spectroscopy analyses demonstrates the chemical action between the functional groups in L-cys and Cu2+. Compared with nickel, zinc and lead ions, copper ions have the strongest binding ability with (-SH), amino (-NH2) and carboxyl (-COOH) groups. This result explains why L-cys can selectively recover copper from leaching solution. This method offers advantages such as fast reaction rates, convenient operating conditions, and enhanced selectivity, which is a promising avenue for the clean and efficient recovery of Cu from discarded PCBs.

Evolution of Wolbachia reproductive and nutritional mutualism: insights from the genomes of two novel strains that double infect the pollinator of dioecious Ficus hirta.

Wolbachia is a genus of maternally inherited endosymbionts that can affect reproduction of their hosts and influence metabolic processes. The pollinator, Valisia javana, is common in the male syconium of the dioecious fig Ficus hirta. Based on a high-quality chromosome-level V. javana genome with PacBio long-read and Illumina short-read sequencing, we discovered a sizeable proportion of Wolbachia sequences and used these to assemble two novel Wolbachia strains belonging to supergroup A. We explored its phylogenetic relationship with described Wolbachia strains based on MLST sequences and the possibility of induction of CI (cytoplasmic incompatibility) in this strain by examining the presence of cif genes known to be responsible for CI in other insects. We also identified mobile genetic elements including prophages and insertion sequences, genes related to biotin synthesis and metabolism. A total of two prophages and 256 insertion sequences were found. The prophage WOjav1 is cryptic (structure incomplete) and WOjav2 is relatively intact. IS5 is the dominant transposon family. At least three pairs of type I cif genes with three copies were found which may cause strong CI although this needs experimental verification; we also considered possible nutritional effects of the Wolbachia by identifying genes related to biotin production, absorption and metabolism. This study provides a resource for further studies of Wolbachia-pollinator-host plant interactions.

Time-Dependent Solvent-Driven Solid-State Fluorescence-based Numeric Coding.

Controllable solid-state transformations can provide a basis for novel functional materials. Herein, we report a series of solid-state systems that can be readily transformed between amorphous, co-crystalline, and mixed crystalline states via grinding or exposure to solvent vapors. The present solid materials were constructed using an all-hydrocarbon macrocycle, cyclo[8](1,3-(4,6-dimethyl)benzene) (D4d-CDMB-8) (host), and neutral aggregation-caused quenching dyes (guests), including 9,10-dibromoanthracene (1), 1,8-naphtholactam (2), diisobutyl perylene-3,9-dicarboxylate (3), 4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (4), 4,7-di(2-thienyl)-benzo[2,1,3]thiadiazole (5), and 4-imino-3-(pyridin-2-yl)-4H-quinolizine-1-carbonitrile (6). Seven co-crystals and six amorphous materials were obtained via host-guest complexation. Most of these materials displayed turn-on fluorescence emission (up to 20-fold enhancement relative to the corresponding solid-state guests). The interconversion between amorphous, co-crystalline states, and crystalline mixtures could be induced by exposure to solvent vapors or by subjecting to grinding. The transformations could be monitored readily by means of single-crystal and powder X-ray diffraction analyses, as well as solid-state fluorescent emission spectroscopy. The externally induced structural interconversions resulted in time-dependent fluorescence changes. This allowed sets of privileged number array codes to be generated.

Phytoplankton Biological Pump Controls the Spatiotemporal Bioaccumulation and Trophic Transfer of Antibiotics in a Large Subtropical River.

The spatiotemporal bioaccumulation, trophic transfer of antibiotics, and regulation of the phytoplankton biological pump were quantitatively evaluated in the Pearl River, South China. The occurrence of antibiotics in organisms indicated a significant spatiotemporal trend associated with the life cycle of phytoplankton. Higher temporal bioaccumulation factors (BAFs) were found in phytoplankton at the bloom site, while lower BAFs of antibiotics in organisms could not be explained by phytoplankton biomass dilution but were attributed to the low bioavailability of antibiotics, which was highly associated with distribution coefficients (R2 = 0.480-0.595, p < 0.05). Such lower BAFs of antibiotics in phytoplankton at higher biomass sites hampered the entry of antibiotics into food webs, and trophic dilutions were subsequently observed for antibiotics except for ciprofloxacin (CFX) and sulfamerazine (SMZ) at sites with blooms in all seasons. Distribution of CFX, norfloxacin (NFX), and sulfapyridine (SPD) showed further significant positive relationships with the plasma protein fraction (R2 = 0.275-0.216, p < 0.05). Both mean BAFs and trophic magnification factors (TMFs) were significantly negatively correlated with phytoplankton biomass (R2 = 0.661-0.741, p < 0.05). This study highlights the importance of the biological pump in the regulation of spatiotemporal variations in bioaccumulation and trophic transfer of antibiotics in anthropogenic-impacted eutrophic rivers in subtropical regions.

The risk of endocarditis in hemodialysis patients who have undergone invasive dental treatment: a cohort case-control analysis of the Taiwan National Health Insurance Database.

OBJECTIVE: The objective of this study was to determine if hemodialysis patients who have undergone an invasive dental treatment are at risk of developing infective endocarditis. MATERIALS AND METHODS: This study was a cohort case-control design and used secondary data collected from the National Health Insurance Research Database of Taiwan. The case group and the control group were each comprised of 19,602 hemodialysis patients. The control group was matched for four variables: age, gender, a medical history of diabetes mellitus, and a cerebrovascular event. After matching, the case group and the control group were each comprised of 19,602 hemodialysis patients. Cox regression analysis determined hazard ratios and 95% confidence intervals. RESULTS: Patients were followed up at 1 month and 3 months after receiving invasive dental treatment. The results showed the cohort case-control hazard ratio was 0.88 (95% CI, 0.49, 1.57) 1 month after receiving invasive dental treatment. Three months after receiving IDT, the cohort case-control hazard ratio was 1.04 (95% CI, 0.71, 1.52). Hazard ratios did not differ significantly between groups. CONCLUSIONS: Hemodialysis patients who received invasive dental treatment had no greater risk of developing infective endocarditis than matched control patients. The results of this study should alleviate concerns for hemodialysis patients and dentists about invasive dental treatment procedures. We recommend hemodialysis patients undergo invasive dental treatment when needed. CLINICAL RELEVANCE: The results of this study showed that invasive dental treatment did not increase their risk of developing infective endocarditis. Hemodialysis patients in need of an invasive dental procedure should be encouraged to undergo treatment if the dentist deems it necessary.

Priming of rhizobial nodulation signaling in the mycosphere accelerates nodulation of legume hosts.

The simultaneous symbiosis of leguminous plants with two root mutualists, endophytic fungi and rhizobia is common in nature, yet how two mutualists interact and co-exist before infecting plants and the concomitant effects on nodulation are less understood. Using a combination of metabolic analysis, fungal deletion mutants and comparative transcriptomics, we demonstrated that Bradyrhizobium and a facultatively biotrophic fungus, Phomopsis liquidambaris, interacted to stimulate fungal flavonoid production, and thereby primed Bradyrhizobial nodulation signaling, enhancing Bradyrhizobial responses to root exudates and leading to early nodulation of peanut (Arachis hypogaea), and such effects were compromised when disturbing fungal flavonoid biosynthesis. Stress sensitivity assays and reactive oxygen species (ROS) determination revealed that flavonoid production acted as a strategy to alleviate hyphal oxidative stress during P. liquidambaris-Bradyrhizobial interactions. By investigating the interactions between P. liquidambaris and a collection of 38 rhizobacteria, from distinct bacterial genera, we additionally showed that the flavonoid-ROS module contributed to the maintenance of fungal and bacterial co-existence, and fungal niche colonization under soil conditions. Our results demonstrate for the first time that rhizobial nodulation signaling can be primed by fungi before symbiosis with host plants and highlight the importance of flavonoid in tripartite interactions between legumes, beneficial fungi and rhizobia.

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers.

With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.

Root endophyte differentially regulates plant response to NO3- and NH4+ nutrition by modulating N fluxes at the plant-fungal interface.

In the soil, plant roots associated with fungi often encounter uneven distribution of nitrate (NO3- )/ammonium (NH4+ ) patches, but the mechanism underlying N form-influenced plant-fungal interactions remains limited. We inoculated Arabidopsis with a root endophyte Phomopsis liquidambaris, and evaluated the effects of P. liquidambaris on plant performance under NO3- or NH4+ nutrition. Under NO3- nutrition, P. liquidambaris inoculation promoted seedling growth, whereas under NH4+ nutrition, P. liquidambaris suppressed seedling growth. Under high NH4+ conditions, fungus-colonized roots displayed increased NH4+ accumulation and NH4+ efflux, similar to the effect of ammonium stress caused by elevated NH4+ levels. Notably, this fungus excluded NH4+ during interactions with host roots, thereby leading to increased NH4+ levels at the plant-fungal interface under high NH4+ conditions. A nitrite reductase-deficient strain that excludes NO3- but absorbs NH4+ , decreased NH4+ levels in Arabidopsis shoots and rescued plant growth and nitrogen metabolism under high NH4+ levels. Transcriptomic analysis highlighted that P. liquidambaris had altered transcriptional responses associated with plant response to inorganic N forms. Our results demonstrate that fungus-regulated NO3- /NH4+ dynamics at the plant-fungal interface alters plant response to NO3- /NH4+ nutrition. This study highlights the essential functions of root endophytes in plant adaptation to soil nitrogen nutrients.

Auricular Vagus Nerve Stimulation Ameliorates Functional Dyspepsia with Depressive-Like Behavior and Inhibits the Hypothalamus-Pituitary-Adrenal Axis in a Rat Model.

BACKGROUND: The hypothalamus-pituitary-adrenal axis is the most important endocrine system to control irritability response. Functional dyspepsia (FD) is closely related to irritability. This study aimed to preliminarily explore the corticotropin-releasing factor (CRF) mechanism of auricular vagus nerve stimulation (aVNS) for FD model rats. METHODS: Sprague-Dawley adult male rats were randomly divided into normal group, model group, aVNS group, and sham-aVNS group. Except for the normal rats, all other rats were induced into the FD model through tail-clamping stimulation for 3 weeks. Once the rat model was developed successfully, rats in the aVNS group and sham-aVNS group were intervened with aVNS or sham-aVNS for 2 weeks. No intervention was given to rats in the normal and model groups. The effect of aVNS was assessed. The expressions of hippocampal corticotropin-releasing hormone receptor 1 (CRHR1), hypothalamus CRF, adrenocorticotropic hormone (ACTH), and corticosterone in serum were assessed. RESULTS: 1. Compared with normal rats, model-developing rats showed FD-like behavior. 2. Compared with model rats, rats in the aVNS group showed an improved general condition score and gastric motility, and increased horizontal and vertical motion scores. 3. The release of corticosterone, ACTH in serum, and CRF in the hypothalamus all increased in model rats but decreased with aVNS instead of sham-aVNS. 4. The expression of hippocampus CRHR1 was lower in model rats but higher in the aVNS group. CONCLUSION: aVNS ameliorates gastric motility and improves the mental state in the FD-like rat, probably via inhibiting the CRF pathway.

Combined System of Organic Substrate and Straw-Degrading Microbial Agents Improved Soil Organic Matter Levels and Microbial Abundance in a Rice-Wheat Rotation.

Rice-wheat rotation is one of the most intensive agricultural planting modes in China and is pivotal to develop optimized straw-returning management in situ to improve soil fertility and productivity in agricultural ecosystems. Previous studies have mainly focused on the effects of straw return with a single application of organic fertilizers. The integrated management of different fertilizers in improving the management of straw return in situ is not well known. In this study, a field experiment was conducted from 2017 to 2019 to explore the effects of a combined system of modified organic substrate (MOS) and straw-degrading compound microbial agent (CMA) on soil physiochemical properties, labile organic carbon, microbial activities, and soil microbial community composition under the background of direct crop straw return and chemical fertilizer utilization. Four treatments were designed: (1) control check; (2) CMA; (3) MOS; and (4) MOS + CMA. The results showed that the MOS + CMA treatment had the combined advantages of soil organic matter (SOM) accumulation, soil nutrient increase and soil microbial community alteration, which may be more suitable for improving the quality and fertility of sandy loam soil. This study provides novel insights for further understanding the effects of organic substrates and composite microbial agents on SOM changes and microbial community composition and function in the field, which has important implications for sustainable crop production and agricultural development.