Data_Sheet_1_Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice.zip

Heterosis has been used widespread in agriculture, but its molecular mechanism is inadequately understood. Plants have a large number of non-coding RNAs (ncRNAs), among them, functional ncRNAs that have been studied widely containing long non-coding RNA (lncRNA) and circular RNA (circRNA) that play a role in varied biological processes, as well as microRNA (miRNA), which can not only regulate the post-transcriptional expression of target genes, but also target lncRNA and circRNA then participate the competing endogenous RNA (ceRNA) regulatory network. However, the influence of these three ncRNAs and their regulatory relationships on heterosis is unknown in rice. In this study, the expression profile of ncRNAs and the ncRNA regulatory network related to heterosis were comprehensively analyzed in inter-subspecific hybrid rice. A total of 867 miRNAs, 3,278 lncRNAs and 2,521 circRNAs were identified in the hybrid and its parents. Analysis of the global profiles of these three types of ncRNAs indicated that significant differences existed in the distribution and sequence characteristics of the corresponding genes. The numbers of miRNA and lncRNA in hybrid were higher than those in its parents. A total of 784 ncRNAs (169 miRNAs, 573 lncRNAs and 42 circRNAs) showed differentially expressed in the hybrid, and their target/host genes were vital in stress tolerance, growth and development in rice. These discoveries suggested that the expression plasticity of ncRNA has an important role of inter-subspecific hybrid rice heterosis. It is worth mentioning that miRNAs exhibited substantially more variations between hybrid and parents compared with observed variation for lncRNA and circRNA. Non-additive expression ncRNAs and allele-specific expression genes-related ncRNAs in hybrid were provided in this study, and multiple sets of ncRNA regulatory networks closely related to heterosis were obtained. Meanwhile, heterosis-related regulatory networks of ceRNA (lncRNA and circRNA) and miRNA were also demonstrated.</p

Selective Separation of Benzene/<i>n</i>‑Hexane with Ester-Functionalized Ionic Liquids

The designer nature of ionic liquids (ILs) has driven their exploration and application in countless fields because of their unique phiscochemical properties. In this work, two ester-functionalized ionic liquids (ILs), <i>N</i>-ethyl acetate-<i>N</i>-methylimidazole bis­(trifluoromethylsulfonyl)­imide ([Eamim]­[NTf₂]) and <i>N</i>-ethyl acetate-<i>N</i>-methylimidazole sulfocyanide­([Eamim]­[SCN]), were prepared. Two ternary systems, benzene-hexane-[Eamim]­[NTf₂] and benzene-hexane-[Eamim]­[SCN], were investigated in terms of both quantum chemical calculation and liquid–liquid extraction experiments. Quantum chemical calculation results showed that the interaction between ILs and benzene was larger than that between ILs with <i>n</i>-hexane. The liquid–liquid extraction results showed that the selectivity reached 29.55 with [Eamim]­[NTf₂], while the selectivity reached 61.44 with [Eamim]­[SCN] at 25 °C. The vapor permeation process was conducted through a supported membrane with ILs. The influences of operating temperature and the feed concentration of benzene were investigated. With the increase of temperature, the selectivity of benzene increased at first and then decreased. When the concentration of benzene was 0.5 and the temperature was 35 °C, the selectivity of benzene reached 16.05, while the flux was 22.14 g·h^–1·m^–2. The stability of the membrane in the vapor permeation was also tested and could remain steady for 60 h

Molecularly Imprinted Electrochemical Sensor Based on α‑Cyclodextrin Inclusion Complex and MXene Modification for Highly Sensitive and Selective Detection of Alkylresorcinols in Whole Wheat Foods

Authenticating whole wheat foods poses a significant challenge for both the grain industry and consumers. Alkylresorcinols (ARs), serving as biomarkers of whole wheat, play a crucial role in assessing the authenticity of whole wheat foods. Herein, we introduce a novel molecularly imprinted electrochemical sensor with modifications involving a molecularly imprinted polymer (MIP) and MXene nanosheets, enabling highly sensitive and selective detection of ARs. Notably, we specifically chose 5-heneicosylresorcinol (AR21), the predominant homologue in whole wheat, as the template molecule. α-Cyclodextrin and acrylamide served as dual functional monomers, establishing a robust multiple interaction between the MIP and AR21. As a result, the sensor exhibited a wide linear range of 0.005 to 100 μg·mL–1 and a low detection limit of 2.52 ng·mL–1, demonstrating exceptional selectivity and stability. When applied to commercial whole wheat foods, the assay achieved satisfactory recoveries and accuracy, strongly validating the practicality and effectiveness of this analytical technique

Highly Specific Bacteriophage-Affinity Strategy for Rapid Separation and Sensitive Detection of Viable Pseudomonas aeruginosa

A virulent bacteriophage highly specific to Pseudomonas aeruginosa (P. aeruginosa) was isolated from hospital sewage using a lambda bacteriophage isolation protocol. The bacteriophage, named as PAP1, was used to functionalize tosyl-activated magnetic beads to establish a bacteriophage-affinity strategy for separation and detection of viable P. aeruginosa. Recognition of the target bacteria by tail fibers and baseplate of the bacteriophage led to capture of P. aeruginosa onto the magnetic beads. After a replication cycle of about 100 min, the progenies lysed the target bacteria and released the intracellular adenosine triphosphate. Subsequently, firefly luciferase-adenosine triphosphate bioluminescence system was used to quantitate the amount of P. aeruginosa. This bacteriophage-affinity strategy for viable P. aeruginosa detection showed a linear range of 6.0 × 10² to 3.0 × 10⁵ CFU mL^–1, with a detection limit of 2.0 × 10² CFU mL^–1. The whole process for separation and detection could be completed after bacteria capture, bacteriophage replication, and bacteria lysis within 2 h. Since the isolated bacteriophage recognized the target bacteria with very high specificity, the proposed strategy did not show any signal response to all of the tested interfering bacteria. Furthermore, it excluded the interference from inactivated P. aeruginosa because the bacteriophage could replicate only in viable cells. The proposed strategy had been applied for detection of P. aeruginosa in glucose injection, human urine, and rat plasma. In the further work, this facile bacteriophage-affinity strategy could be extended for detection of other pathogens by utilizing virulent bacteriophage specific to other targets

Identification of a protective B-cell epitope of the <i>Staphylococcus aureus</i> GapC protein by screening a phage-displayed random peptide library

<div><p>The impact of epidemic <i>Staphylococcus aureus</i> (<i>S</i>. <i>aureus</i>) on public health is increasing. Because of the abuse of antibiotics, the antibiotic resistance of <i>S</i>. <i>aureus</i> is increasing. Thus, there is an urgent need to develop new immunotherapies and immunoprophylaxes. Previous studies showed that the GapC protein of <i>S</i>. <i>aureus</i>, which is a surface protein with high glyceraldehyde 3-phosphate dehydrogenase activity, transferrin binding activity, and other biological activities, is highly conserved. GapC induces an effective humoral immune response <i>in vivo</i>. However, the B-cell epitopes of <i>S</i>. <i>aureus</i> GapC have not been well identified. Here we used the bioinformatics tools to analyze the sequence of GapC, and we generated protective anti-GapC monoclonal antibodies (mAbs). A protective mAb (1F4) showed strong specificity to GapC and the ability to induce macrophages to phagocytose <i>S</i>. <i>aureus</i>. We screened the motif ²⁷²GYTEDEIVSSD²⁸², which was recognized by mAb 1F4, using a phage display system. Then, we used site-directed mutagenesis to identify key amino acids in the motif. Residues G272 D276 E277 I278 and V279 formed the core of the ²⁷²GYTEDEIVSSD²⁸² motif. In addition, we showed that this epitope peptide induced a protective humoral immune response against <i>S</i>. <i>aureus</i> infection in immunized mice. Our results will be useful for the further study of epitope-based vaccines against <i>S</i>. <i>aureus</i> infection.</p></div

anti-epitope serum-mediated phagocytosis of S. <i>aureus</i> Newman.

<p>PBS-washed Newman (2×10⁵ CFU) was incubated with 50 μl of the serum for 30 min. The negative control was incubated with the negative serum and the blank control comprised only phagocytes and bacteria. Differences in the internalization rates between anti-epitope peptide serum group and anti-negative serum group was statistically significant. The data represent the means ± SEM (<i>n</i> = 3). Statistical significance was measured using a Student’s t-test (**, <i>p</i> < 0.01).</p

The ²⁷²GYTEDEIV²⁷⁹ epitope peptide confers protection against lethal challenges with <i>S</i>. <i>aureus</i> Newman.

<p>For the prophylaxis study, immunized and control mice (6 weeks old, <i>n</i> = 10) were challenged intraperitoneally with <i>S</i>. <i>aureus</i> (equivalent to 5 × 10⁸ CFU) two weeks after the last immunization. Mice were monitored for 15 days. The survival rates of GapC, GST-epitope were 70% and 50%, respectively. Statistical differences were determined by Student’s t-test. (***, <i>p</i> < 0.001).</p

Characterization of mAbs.

<p>(<b>a</b>) The purified 1F4 was analyzed by 12% SDS-PAGE. (<b>b</b>) GapC recognized by the mAb 1F4 was detected by western blotting. (<b>c</b>) The class of the mAb 1F4 was determined to be IgG1 and the κ chain. (<b>d</b>) The specificity of mAb 1F4 toward recombinant FnbpA,Trap, Mntc, IsdB of <i>S</i>. <i>aureus</i> and GapC from <i>S</i>. <i>dysgalactiae</i> was determined by indirect ELISA. (<b>e</b>) The reactivity of mAb 1F4 with the recombinant FnbpA, Trap, Mntc, IsdB proteins of <i>S</i>. <i>aureus</i> and GapC from <i>S</i>. <i>dysgalactiae</i> was determined by western blotting. (<b>f</b>) Effect of 1F4 on GapC GAPDH activity of <i>S</i>. <i>aureus</i>. The OD values were detected at 20 s (A1) and 5 min and 20 s (A2), the decrease of NADH reflected the level of GAPDH activity at <i>OD</i>₃₄₀. The data represent the means ± SEM (<i>n</i> = 3). (<b>g</b>) Passive immunization with mAb 1F4 protects against <i>S</i>. <i>aureus</i> infection. Mice were injected intraperitoneally with 5×10⁸ CFU of <i>S</i>. <i>aureus</i> (Newman) followed by the intravenous injection of anti-GapC serum, mAb 1F4, or SP2/0 cell supernatant (nagative control) after 24 h (<i>n</i> = 10).</p

Precisely defining the epitopes.

<p>The reactivity of the fusion proteins, in which each amino acid (²⁷¹FGYTEDEIVS²⁸⁰) was mutated to alanine, with mAb 1F4 was identified by western blotting. The G272A, D276A, E277A, I278A, and V279A mutations completely disrupted the reactivity of the epitope with mAb 1F4.</p

Analysis of the ²⁷²GYTEDEIV²⁷⁹ epitope by confocal laser-scanning microscopy.

<p>The left panels show dark field fluorescence photos; the middle panels show bright field photos of the bacteria; and the right panels show the two fields combined. (<b>a–c</b>) The <i>S</i>. <i>aureus</i> (Newman) strain was observed. Primary antibodies were <i>S</i>. <i>aureus</i> anti-GapC serum, mAb 1F4, and the SP2/0 supernatant, respectively.</p