Layered CrO2·nH2O as a cathode material for aqueous zinc-ion batteries: ab initio study.

Aqueous zinc-ion batteries are considered potential large-scale energy storage systems due to their low cost, environmentally friendly nature, and high safety. However, the development of high energy density cathode materials and uncertain reaction mechanisms remains a major challenge. In this work, the reaction mechanism, discharge voltage and diffusion properties of layered CrO2 as a cathode material for aqueous zinc-ion batteries were studied using first-principles calculations, and the effect of pre-intercalated structural water on the electrochemical performance of CrO2 electrodes is also discussed. The results show that CrO2 exhibits high average discharge voltages (2.65 V for H insertion (pH = 7) and 1.97 V for Zn insertion) and medium theoretical capacities (319 mA h g-1 (H and Zn)). The H intercalation voltage strongly depends on the pH value of the electrolyte. The H/Zn co-insertion mechanism occurs at low hydrogen concentrations (c(H) ≤ 0.125), where the initial insertion of H reduces the total amount of subsequent Zn insertion. For the substrate containing structured water (CrO2·nH2O, n ≥ 0.5), the average voltage of Zn insertion is significantly increased, while the average voltage of H slightly decreases. In addition, the pre-intercalated water strategy significantly improved the diffusion properties of H and Zn. This study shows that layered CrO2·nH2O is a promising cathode material for aqueous zinc-ion batteries, and also provides theoretical guidance for the development of high-performance cathode materials for aqueous zinc-ion batteries.

Physiological, transcriptomic, and metabolomic analyses reveal that Pantoea sp. YSD J2 inoculation improves the accumulation of flavonoids in Cyperus esculentus L. var. sativus.

Plant growth-promoting microorganisms (PGPMs), such as Pantoea sp. YSD J2, promote plant development and stress resistance, while their role in flavonoids accumulation still needs to be further understood. To investigate the complex flavonoid biosynthesis pathway of Cyperus esculentus L. var. sativus (tigernut), we compared Pantoea sp. YSD J2 inoculation (YSD J2) and water inoculation (CK) groups. YSD J2 significantly elevated the content of indole-3-acetic acid (IAA) and orientin. Furthermore, when analyzing flavonoid metabolome, YSD J2 caused increased levels of uralenol, petunidin-3-O-glucoside-5-O-arabinoside, luteolin-7-O-glucuronide-(2 â†’ 1)-glucuronide, kaempferol-3-O-neohesperidoside, cyanidin-3-O-(2″-O-glucosyl)glucoside, kaempferol-3-O-glucuronide-7-O-glucoside, quercetin-3-O-glucoside, luteolin-7-O-glucuronide-(2 â†’ 1)-(2″-sinapoyl)glucuronide, and quercetin-4'-O-glucoside, which further enhanced antioxidant activity. We then performed RNA-seq and LC-MS/MS, aiming to validate key genes and related flavonoid metabolites under YSD J2 inoculation, and rebuild the gene-metabolites regulatory subnetworks. Furthermore, the expression patterns of the trans cinnamate 4-monooxygenase (CYP73A), flavonol-3-O-L-rhamnoside-7-O-glucosyltransferase (UGT73C6), shikimate O-hydroxycinnamoyltransferase (HCT), chalcone isomerase (CHI), flavonol synthase (FLS), and anthocyanidin synthase (ANS) genes were confirmed by qRT-PCR. Additionally, 4 transcription factors (TF) (especially bHLH34, Cluster-37505.3) under YSD J2 inoculation are also engaged in regulating flavonoid accumulation. Moreover, the current work sheds new light on studying the regulatory effect of Pantoea sp. YSD J2 on tigernut development and flavonoid biosynthesis.

Effect of Nitrogen on Precipitate Characteristics and Pitting Resistance of Martensitic Stainless Steel.

High-carbon-chromium martensitic stainless steel (MSS) is widely used in many fields due to its excellent mechanical properties, while the coarse eutectic carbide in MSS deteriorates corrosion resistance. In this work, nitrogen was added to the MSS to improve corrosion resistance. The effects of nitrogen on the microstructure and corrosion resistance of MSS were systematically studied. The results showed that the addition of nitrogen promoted the development of Cr2N and reversed austenite, effectively inhibiting the formation of δ-ferrite. Therefore, the durability of the passivation film was improved, the passivation zone was expanded, and the susceptibility to metastable pitting was decreased. As a consequence, nearly two orders of magnitude have been achieved in the pitting potential (Epit) of MSS containing nitrogen, and the polarization resistance value (Rp) has gone up from 4.05 kΩ·cm2 to 1.24 × 102 kΩ·cm2. This means that in a corrosive environment, nitrogen-treated MSS stainless steel is less likely to form pitting pits, which further extends the service life of the material.

Multiple Perspectives of Study on the Potential of Bacillus amyloliquefaciens JB20221020 for Alleviating Nutrient Stress in Lettuce.

Soil nutrient deficiency has become a key factor limiting crop growth. Plant growth-promoting rhizobacteria (PGPR) are vital in resisting abiotic stress. In this study, we investigated the effects of inoculation with Bacillus amyloliquefaciens JB20221020 on the physiology, biochemistry, rhizosphere microorganisms, and metabolism of lettuce under nutrient stress. Pot experiments showed that inoculation with B. amyloliquefaciens JB20221020 significantly promoted lettuce growth under nutrient deficiency. At the same time, the activities of the antioxidant enzymes superoxide dismutase, peroxidase, and catalase and the content of proline increased, and the content of Malondialdehyde decreased in the lettuce inoculated with B. amyloliquefaciens JB20221020. Inoculation with B. amyloliquefaciens JB20221020 altered the microbial community of the rhizosphere and increased the relative abundances of Myxococcales, Deltaproteobacteria, Proteobacteria, Devosia, and Verrucomicrobia. Inoculation also altered the rhizosphere metabolism under nutrient deficiency. The folate metabolism pathway was significantly enriched in the Kyoto Encyclopedia of Genes and Genomes enrichment analysis. This study explored the interaction between plants and microorganisms under nutrient deficiency, further explained the critical role of rhizosphere microorganisms in the process of plant nutrient stress, and provided a theoretical basis for the use of microorganisms to improve plant resistance.

Revealing the ACE receptor binding properties and interaction mechanisms of salty oligopeptides from Stropharia rugosoannulata mushroom by molecular simulation and antihypertensive evaluation.

The salty oligopeptides from Stropharia rugosoannulata have been proven to be potential ACE inhibitors. To investigate the ACE receptor binding properties and interaction mechanisms of salty oligopeptides, the molecular interaction, dynamics simulation, and antihypertensive evaluation cross-validation strategy were employed to reveal the oligopeptides' binding reactions and modes with the ACE receptor. Single oligopeptide (ESPERPFL, KSWDDFFTR) had exothermic and specific binding reactions with the ACE receptor, driven by hydrogen bonds and van der Waals forces. The coexistence of the multiple oligopeptide molecules did not produce the apparent ACE receptor competition binding reactions. The molecular dynamics simulation verified that the two oligopeptides disturbed the ACE receptor's different residue regions. Both oligopeptides could form stable complexes with the ACE receptor. Based on the classification of 50 oligopeptides' binding modes, ESPERPFL and KSWDDFFTR belonged to different classes, and their receptor binding modes and sites complemented, resulting in a potential synergistic effect on ACE inhibition. The antihypertensive effect of KSWDDFFTR and its distribution in the body were evaluated using SHR rats orally and ICR mice by tail vein injection, and KSWDDFFTR had antihypertensive effects within 8 h. The study provides a theoretical basis for understanding salty oligopeptides' ACE receptor binding mechanism and their antihypertensive effects.

Long noncoding RNAs underlie multiple domestication traits and leafhopper resistance in soybean.

The origin and functionality of long noncoding RNA (lncRNA) remain poorly understood. Here, we show that multiple quantitative trait loci modulating distinct domestication traits in soybeans are pleiotropic effects of a locus composed of two tandem lncRNA genes. These lncRNA genes, each containing two inverted repeats, originating from coding sequences of the MYB genes, function in wild soybeans by generating clusters of small RNA (sRNA) species that inhibit the expression of their MYB gene relatives through post-transcriptional regulation. By contrast, the expression of lncRNA genes in cultivated soybeans is severely repressed, and, consequently, the corresponding MYB genes are highly expressed, shaping multiple distinct domestication traits as well as leafhopper resistance. The inverted repeats were formed before the divergence of the Glycine genus from the Phaseolus-Vigna lineage and exhibit strong structure-function constraints. This study exemplifies a type of target for selection during plant domestication and identifies mechanisms of lncRNA formation and action.

A Dual-mode platform for the rapid detection of Escherichia coli O157:H7 based on CRISPR/Cas12a and RPA.

Escherichia coli O157:H7 (E. coli O157:H7) is a foodborne pathogenic microorganism that is commonly found in the environment and poses a significant threat to human health, public safety, and economic stability worldwide. Thus, early detection is essential for E. coli O157:H7 control. In recent years, a series of E. coli O157:H7 detection methods have been developed, but the sensitivity and portability of the methods still need improvement. Therefore, in this study, a rapid and efficient testing platform based on the CRISPR/Cas12a cleavage reaction was constructed. Through the integration of recombinant polymerase amplification and lateral flow chromatography, we established a dual-interpretation-mode detection platform based on CRISPR/Cas12a-derived fluorescence and lateral flow chromatography for the detection of E. coli O157:H7. For the fluorescence detection method, the limits of detection (LODs) of genomic DNA and E. coli O157:H7 were 1.8 fg/µL and 2.4 CFU/mL, respectively, within 40 min. Conversely, for the lateral flow detection method, LODs of 1.8 fg/µL and 2.4 × 102 CFU/mL were achieved for genomic DNA and E. coli O157:H7, respectively, within 45 min. This detection strategy offered higher sensitivity and lower equipment requirements than industry standards. In conclusion, the established platform showed excellent specificity and strong universality. Modifying the target gene and its primers can broaden the platform's applicability to detect various other foodborne pathogens.

Using multi-omics to explore the effect of Bacillus velezensis SAAS-63 on resisting nutrient stress in lettuce.

To avoid the unreasonable use of chemical fertilizer, an environmentally friendly means of improving soil fertility is required. This study explored the role of the plant growth-promoting rhizosphere bacteria (PGPR) strain Bacillus velezensis SAAS-63 in improving nutrient stress in lettuce. Compared with no inoculation, B. velezensis SAAS-63 inoculants exhibited significantly increased fresh weight, root length, and shoot height under nutrient deficiency, as well as improved antioxidant activities and proline contents. The exogenous addition of B. velezensis SAAS-63 also significantly increased the accumulation of macroelements and micronutrients in lettuce. To elucidate the resistance mechanisms induced by B. velezensis SAAS-63 under nutrient stress, high-throughput sequencing and multi-omics analysis were performed. Inoculation with B. velezensis SAAS-63 altered the microbial community of the rhizosphere and increased the relative abundances of Streptomyces, Actinoallomurus, Verrucomicrobia, and Chloroflexi. It is worth noting that the inoculant SAAS-63 can affect plant rhizosphere metabolism. The inoculant changed the metabolic flow of phenylpropanoid metabolic pathway under nutrient deficiency and promoted phenylalanine to participate more in the synthesis of lignin precursors and coumarin substances by inhibiting the synthesis of flavone and isoflavone, thus improving plant resistance. This study showed that the addition of inoculant SAAS-63 could help plants recruit microorganisms to decompose and utilize trehalose and re-established the carbon metabolism of the plant rhizosphere. Additionally, microbes were found to be closely related to the accumulation of metabolites based on correlation analysis. The results indicated that the addition of PGPRs has an important role in regulating soil rhizosphere microbes and metabolism, providing valuable information for understanding how PGPRs affect complex biological processes and enhance plant adaptation to nutrient deficiency. KEY POINTS: • Inoculation with SAAS-63 significantly promoted plant growth under nutrient-deficient conditions • Inoculation with SAAS-63 affected rhizosphere microbial diversity and community structure • Inoculation with SAAS-63 affected plant rhizosphere metabolism and induced plants to synthesize substances that resist stress.

Microstructure Evolution, Hot Deformation Behavior and Processing Maps of an FeCrAl Alloy.

The deteriorated plasticity arising from the insoluble precipitates may lead to cracks during the rolling of FeCrAl alloys. The microstructure evolution and hot deformation behavior of an FeCrAl alloy were investigated in the temperature range of 750-1200 °C and strain rate range of 0.01-10 s-1. The flow stress of the FeCrAl alloy decreased with an increasing deformation temperature and decreased strain rate during hot working. The thermal deformation activation energy was determined to be 329.49 kJ/mol based on the compression test. Then, the optimal hot working range was given based on the established hot processing maps. The hot processing map revealed four small instability zones. The optimal working range for the material was identified as follows: at a true strain of 0.69, the deformation temperature should be 1050-1200 °C, and the strain rate should be 0.01-0.4 s-1. The observation of key samples of thermally simulated compression showed that discontinuous dynamic recrystallization started to occur with the temperate above 1000 °C, leading to bended grain boundaries. When the temperature was increased to 1150 °C, the dynamic recrystallization resulted in a microstructure composed of fine and equiaxed grains.

Research Note: Effects of the intermittent feeding of microencapsulation essential oil on laying performance, egg quality, immune response, intestinal morphology, and oxidation status of laying hens.

The aim of this study was to evaluate the effect of microencapsulated essential oils (MEO) on the laying performance, egg quality, immunity, intestinal morphology, and oxidative status of laying hens. A total of 640 Hy-line Brown laying hens, 41 wk of age, were randomly divided into 4 groups, each with 8 replicates containing 20 birds per replicate. The dietary conditions tested included a basal diet (Control) or the basal diet supplemented with various levels of MEO at 100 mg/kg (MEO100), 300 mg/kg (MEO300), and 500 mg/kg (MEO500). The three treatment groups were intermittently fed MEO, following an alternating schedule of 1 wk on and 1 wk off for a total of 56 d. Results showed that feeding MEO at levels of 300 and 500 mg/kg improved both egg production and feed conversion ratios compared to the control group. Hens consumed MEO-supplemented diets exhibited a significant decrease in the breaking egg ratio (P < 0.05) compared to those fed the control diet. Shell thickness and Haugh unit values significantly increased in the groups receiving 300 and 500 mg/kg of MEO (P < 0.05). Both the MEO300 and MEO500 treatments led to improvements in immunoglobulin (IgA, IgM, and IgG) and cytokine (IL-2 and IFN-γ) levels in serum. Hens in the MEO300 and MEO500 groups exhibited higher values for parameters related to intestinal morphometry compared to the control group. Furthermore, supplementation with 300 and 500 mg/kg of MEO enhanced the antioxidant capacity of plasma, as evidenced by increased activities of glutathione peroxidase (GSH-Px), total superoxide dismutase (T-SOD), and catalase (CAT) (P < 0.05). In summary, the intermittent feeding of MEO improved egg production, enhanced antioxidative processes, immune functions, and intestinal morphology, leading to an amelioration in the egg quality of laying hens. Our data demonstrate that supplementation of 300 mg/kg of MEO in feed can significantly improve animal health and egg quality. Implementation of these feeding practices could have a positive economic impact on poultry and egg industry.

Isothermal Amplification and CRISPR/Cas12a-System-Based Assay for Rapid, Sensitive and Visual Detection of Staphylococcus aureus.

Staphylococcus aureus exists widely in the natural environment and is one of the main food-borne pathogenic microorganisms causing human bacteremia. For safe food management, a rapid, high-specificity, sensitive method for the detection of S. aureus should be developed. In this study, a platform for detecting S. aureus (nuc gene) based on isothermal amplification (loop-mediated isothermal amplification-LAMP, recombinase polymerase amplification-RPA) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas12a) proteins system (LAMP, RPA-CRISPR/Cas12a) was proposed. In this study, the LAMP, RPA-CRISPR/Cas12a detection platform and immunochromatographic test strip (ICS) were combined to achieve a low-cost, simple and visualized detection of S. aureus. The limit of visual detection was 57.8 fg/µL of nuc DNA and 6.7 × 102 CFU/mL of bacteria. Moreover, the platform could be combined with fluorescence detection, namely LAMP, RPA-CRISPR/Cas12a-flu, to establish a rapid and highly sensitive method for the detection of S. aureus. The limit of fluorescence detection was 5.78 fg/µL of genomic DNA and 67 CFU/mL of S. aureus. In addition, this detection platform can detect S. aureus in dairy products, and the detection time was ~40 min. Consequently, the isothermal amplification CRISPR/Cas12a platform is a useful tool for the rapid and sensitive detection of S. aureus in food.

Self-Recovery of a Buckling BaTiO3 Ferroelectric Membrane.

The characteristic of self-recovery holds significant implications for upholding performance stability within flexible electronic devices following the release of mechanical deformation. Herein, the dynamics of self-recovery in a buckling inorganic membrane is studied via in situ scanning probe microscopy technology. The experimental results demonstrate that the ultimate deformation ratio of the buckling BaTiO3 ferroelectric membrane is up to 88%, which is much higher than that of the buckling SrTiO3 dielectric membrane (49%). Combined with piezoresponse force microscopy and phase-field simulations, we find that ferroelectric domain transformation accompanies the whole process of buckling and self-recovery of the ferroelectric membrane, i.e., the presence of the nano-c domain not only releases part of the elastic energy of the membrane but also reduces the interface mismatch of the a/c domain, which encourages the buckling ferroelectric membrane to have excellent self-recovery properties. It is conceivable that the evolution of ferroelectric domains will play a greater role in the regulation of the mechanical properties of ferroelectric membranes and flexible devices.

A rapid and high-throughput system for the detection of transgenic products based on LAMP-CRISPR-Cas12a.

With the increasing acreage of genetically modified crops worldwide, rapid and efficient detection technologies have become very important for the regulation and screening of GM organisms. We constructed a method based on loop-mediated isothermal amplification (LAMP), CRISPR-Cas12a and lateral flow assay (LAMP-CRISPR-Cas12a-LFA). It is an intuitive, sensitive and specific fluorescence detection and test strip system to detect CP4-EPSPS and Cry1Ab/Ac genes in field screening. The LAMP-CRISPR-Cas12a-LFA method has a limit of detection (LOD) of 100 copies based on lateral flow test strips after optimization of the conditions with screened specific primers, and the entire detection process can be completed within 1 h at 61 °C. The system was used to evaluate field test samples and showed high reproducibility after testing products containing CP4-EPSPS and Cry1Ab/Ac genes, and both were detectable. The LAMP-CRISPR-Cas12a-LFA method established in this paper functions as a rapid field detection method. It requires only one portable thermostatic instrument, which renders it compatible with the rapid detection of field samples and useable at experimental workstations, in law enforcement field work, and in local inspection and quarantine departments.

Structure-Activity Relationship of Novel ACE Inhibitory Undecapeptides from Stropharia rugosoannulata by Molecular Interactions and Activity Analyses.

Undecapeptide is the central peptide molecule in the peptide base material of Stropharia rugosoannulata, and angiotensin-converting enzyme (ACE) plays a crucial role in hypertension. To fully explore the interaction mechanism and ACE-inhibitory activity of long-chain peptides from Stropharia rugosoannulata, the binding conformations of twenty-seven undecapeptides with the ACE receptor were revealed by molecule docking. The undecapeptide GQEDYDRLRPL with better receptor binding capacity and higher secondary mass spectral abundance was screened. All amino acid residues except proline in GQEDYDRLRPL interacted with the ACE receptor. GQEDYDRLRPL interfered with the receptor's overall structure, with significant fluctuations in amino acid residues 340-355, including two residues in the receptor's active pockets. The binding constants of GQEDYDRLRPL to the ACE receptors were at the µM level, with a kinetic binding constant of 9.26 × 10-7 M, which is a strong binding, and a thermodynamic binding constant of 3.06 × 10-6 M. Intermolecular interaction were exothermic, enthalpy-driven, and specific binding reactions. GQEDYDRLRPL had an IC50 value of 164.41 µmol/L in vitro and superior antihypertensive effects at low-gavage administration in vivo. Obtaining information on the interaction mechanism of ACE-inhibitory undecapeptides from S. rugosoannulata with the ACE receptor will help to develop and utilize ACE inhibitors of natural origin.

Visual-quality-driven unsupervised image dehazing.

Most of the existing learning-based dehazing methods require a diverse and large collection of paired hazy/clean images, which is intractable to obtain. Therefore, existing dehazing methods resort to training on synthetic images. This may result in a possible domain shift when treating real scenes. In this paper, we propose a novel unsupervised dehazing (lightweight) network without any reference images to directly predict clear images from the original hazy images, which consists of an interactive fusion module (IFM) and an iterative optimization module (IOM). Specifically, IFM interactively fuses multi-level features to make up for the missing information among deep and shallow features while IOM iteratively optimizes dehazed results to obtain pleasing visual effects. Particularly, based on the observation that hazy images usually suffer from quality degradation, four non-reference visual-quality-driven loss functions are designed to enable the network trained in an unsupervised way, including dark channel loss, contrast loss, saturation loss, and edge sharpness loss. Extensive experiments on two synthetic datasets and one real-world dataset demonstrate that our method performs favorably against the state-of-the-art unsupervised dehazing methods and even matches some supervised methods in terms of metrics such as PSNR, SSIM, and UQI.

Two electrochemiluminescence immunosensors for the sensitive and quantitative detection of the CP4-EPSPS protein in genetically modified crops.

Two different models of electrochemiluminescence (ECL) immunosensors for the sensitive and quantitative detection of the CP4-EPSPS protein in genetically modified (GM) crops were proposed in this study. One was a signal-reduced ECL immunosensor based on nitrogen-doped graphene, graphitic carbon nitride and polyamide-amine (GN-PAMAM-g-C3N4) composites as the electrochemically active substance. The other model was a signal-enhanced ECL immunosensor based on a GN-PAMAM modified electrode for the detection of CdSe/ZnS quantum dots (QDs)-labeled antigens. The ECL signal responses of the reduced and enhanced immunosensors linearly decreased as the increase of the soybean RRS and RRS-QDs content in the range of 0.05% to 1.5% and 0.025% to 1.0%, with the limits of detection of 0.03% and 0.01% (S/N = 3), respectively. Both of the ECL immunosensors showed good specificity, stability, accuracy, and reproducibility in the analysis of real samples. The results indicate that the two immunosensors provide an ultra-sensitive and quantitative approach for the determination of the CP4-EPSPS protein. Due to their outstanding performances, the two ECL immunosensors could be useful tools for achieving the effective regulation of GM crops.

Ureterocele with duplex collecting systems and febrile urinary tract infection risk.

PURPOSE: Ureterocele has been hypothesized to be the risk factor for febrile urinary tract infections (F-UTIs) in patients with duplex collecting systems, but this has not been proved, and our goal was to assess the relation between ureterocele with duplex collecting systems and F-UTIs. METHODS: We included individual-participant data from patients seen for complicated duplex collecting systems from 2010 to 2020 retrospectively followed. Those with using continuous low-dose antibiotic prophylaxis and incompletely duplicated systems were removed from the study. The participants were divided into two cohorts according to patients with or without ureterocele. The primary endpoint of this study was recurrent F-UTIs. RESULTS: We analyzed medical reports of 300 patients, of which 75% were female. Among the 300 patients, F-UTIs developed in 111/159 (69.8%) patients in the ureterocele group and in 69/141 (48.9%) patients in the no-ureterocele group. Univariate analysis found no discernible difference except in grade of hydronephrosis between ureterocele group and no-ureterocele group. Moreover, Cox proportional regression analysis revealed that patients of duplex system ureterocele might be intrinsically more prone to develop F-UTIs (adjusted hazard ratio 1.894; 95% CI 1.412-2.542; p  <  0.001). CONCLUSION: Among participants with duplex systems, the risk of recurrent F-UTIs in patients with ureterocele was higher than patients without it, and mini-invasive surgical correction should be considered at young age to reduce F-UTIs.

Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae).

BACKGROUND: Analysis of the relationship between chromosomal structural variation (synteny breaks) and 3D-chromatin architectural changes among closely related species has the potential to reveal causes and correlates between chromosomal change and chromatin remodeling. Of note, contrary to extensive studies in animal species, the pace and pattern of chromatin architectural changes following the speciation of plants remain unexplored; moreover, there is little exploration of the occurrence of synteny breaks in the context of multiple genome topological hierarchies within the same model species. RESULTS: Here we used Hi-C and epigenomic analyses to characterize and compare the profiles of hierarchical chromatin architectural features in representative species of the cotton tribe (Gossypieae), including Gossypium arboreum, Gossypium raimondii, and Gossypioides kirkii, which differ with respect to chromosome rearrangements. We found that (i) overall chromatin architectural territories were preserved in Gossypioides and Gossypium, which was reflected in their similar intra-chromosomal contact patterns and spatial chromosomal distributions; (ii) the non-random preferential occurrence of synteny breaks in A compartment significantly associate with the B-to-A compartment switch in syntenic blocks flanking synteny breaks; (iii) synteny changes co-localize with open-chromatin boundaries of topologically associating domains, while TAD stabilization has a greater influence on regulating orthologous expression divergence than do rearrangements; and (iv) rearranged chromosome segments largely maintain ancestral in-cis interactions. CONCLUSIONS: Our findings provide insights into the non-random occurrence of epigenomic remodeling relative to the genomic landscape and its evolutionary and functional connections to alterations of hierarchical chromatin architecture, on a known evolutionary timescale.

Combined metagenomic and metabolomic analyses reveal that Bt rice planting alters soil C-N metabolism.

The environmental impacts of genetically modified (GM) plants remain a controversial global issue. To address these issues, comprehensive environmental risk assessments of GM plants is critical for the sustainable development and application of transgenic technology. In this paper, significant differences were not observed between microbial metagenomic and metabolomic profiles in surface waters of the Bt rice (T1C-1, the transgenic line) and non-Bt cultivars (Minghui 63 (the isogenic line) and Zhonghua 11 (the conventional japonica cultivar)). In contrast, differences in these profiles were apparent in the rhizospheres. T1C-1 planting increased soil microbiome diversity and network stability, but did not significantly alter the abundances of potential probiotic or phytopathogenic microorganisms compared with Minghui 63 and Zhonghua 11, which revealed no adverse effects of T1C-1 on soil microbial communities. T1C-1 planting could significantly alter soil C and N, probably via the regulation of the abundances of enzymes related to soil C and N cycling. In addition, integrated multi-omic analysis of root exudate metabolomes and soil microbiomes showed that the abundances of various metabolites released as root exudates were significantly correlated with subsets of microbial populations including the Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes that were differentially abundant in T1C-1 and Mnghui 63 soils. Finally, the potential for T1C-1-associated root metabolites to exert growth effects on T1C-1-associated species was experimentally validated by analysis of bacterial cultures, revealing that Bt rice planting could selectively modulate specific root microbiota. Overall, this study indicate that Bt rice can directly modulate rhizosphere microbiome assemblages by altering the metabolic compositions of root exudates that then alters soil metabolite profiles and physiochemical properties. This study unveils the mechanistic associations of Bt plant-microorganism-environment, which provides comprehensive insights into the potential ecological impacts of GM plants.

A rapid and high-throughput Helicobacter pylori RPA-CRISPR/Cas12a-based nucleic acid detection system.

BACKGROUND: Helicobacter pylori lives in the human stomach and causes gastric cancer and other gastric diseases. The development of molecular technology has facilitated low-cost, rapid, and high-throughput detection of H. pylori. MATERIALS AND METHODS: The combination of isothermal recombinase polymerase amplification (RPA) and CRISPR-Cas12a was used for early diagnosis and monitoring of H. pylori in clinical settings. The UreB genes from 242 H. pylori strains were subjected to cluster analysis, and we designed corresponding RPA primers and screened 2 sets of CRISPR-derived RNAs (crRNAs) for accurate H. pylori recognition. We then performed specificity and sensitivity validation of seven strains using this RPA-CRISPR/Cas12a method. In addition, the cut-off values of this RPA-CRISPR/Cas12a method based on fluorescence values (i.e., RPA-CRISPR/Cas12a-FT) were determined by comparison with quantitative PCR (qPCR), and further experiments comparing different methods were performed using clinical samples. RESULTS: We developed a rapid detection system based on the combination of RPA and CRISPR-Cas12a, which was applied to the early diagnosis and monitoring of H. pylori in clinical settings. The RPA-CRISPR/Cas12a system was used to detect the UreB gene. We found that the limit of detection (LOD) for the CRISPR/Cas12a method based on the lateral flow dipstick result (i.e., CRISPR/Cas12a-LFD) was 100 copies, the cut-off value was 1.4; and for CRISPR/Cas12a-FT the LOD was 50 copies. This system was used to assess clinical samples and showed high reproducibility with proof-of-concept sensitivity, and the whole detection process was completed within 40 min. CONCLUSION: As a diagnostic method that can detect the UreB gene of H. pylori in gastric tissue samples rapidly, sensitively, visually, and in a high throughput manner, our method provides a new diagnostic option for clinicians. This system is ideal for hospitals or testing sites with limited medical resources.