Susceptibility gene identification and risk evaluation model construction by transcriptome-wide association analysis for salt sensitivity of blood pressure.

BACKGROUND: Salt sensitivity of blood pressure (SSBP) is an intermediate phenotype of hypertension and is a predictor of long-term cardiovascular events and death. However, the genetic structures of SSBP are uncertain, and it is difficult to precisely diagnose SSBP in population. So, we aimed to identify genes related to susceptibility to the SSBP, construct a risk evaluation model, and explore the potential functions of these genes. METHODS AND RESULTS: A genome-wide association study of the systemic epidemiology of salt sensitivity (EpiSS) cohort was performed to obtain summary statistics for SSBP. Then, we conducted a transcriptome-wide association study (TWAS) of 12 tissues using FUSION software to predict the genes associated with SSBP and verified the genes with an mRNA microarray. The potential roles of the genes were explored. Risk evaluation models of SSBP were constructed based on the serial P value thresholds of polygenetic risk scores (PRSs), polygenic transcriptome risk scores (PTRSs) and their combinations of the identified genes and genetic variants from the TWAS. The TWAS revealed that 2605 genes were significantly associated with SSBP. Among these genes, 69 were differentially expressed according to the microarray analysis. The functional analysis showed that the genes identified in the TWAS were enriched in metabolic process pathways. The PRSs were correlated with PTRSs in the heart atrial appendage, adrenal gland, EBV-transformed lymphocytes, pituitary, artery coronary, artery tibial and whole blood. Multiple logistic regression models revealed that a PRS of P < 0.05 had the best predictive ability compared with other PRSs and PTRSs. The combinations of PRSs and PTRSs did not significantly increase the prediction accuracy of SSBP in the training and validation datasets. CONCLUSIONS: Several known and novel susceptibility genes for SSBP were identified via multitissue TWAS analysis. The risk evaluation model constructed with the PRS of susceptibility genes showed better diagnostic performance than the transcript levels, which could be applied to screen for SSBP high-risk individuals.

DNMT3L inhibits hepatocellular carcinoma progression through DNA methylation of CDO1: insights from big data to basic research.

BACKGROUND: DNMT3L is a crucial DNA methylation regulatory factor, yet its function and mechanism in hepatocellular carcinoma (HCC) remain poorly understood. Bioinformatics-based big data analysis has increasingly gained significance in cancer research. Therefore, this study aims to elucidate the role of DNMT3L in HCC by integrating big data analysis with experimental validation. METHODS: Dozens of HCC datasets were collected to analyze the expression of DNMT3L and its relationship with prognostic indicators, and were used for molecular regulatory relationship evaluation. The effects of DNMT3L on the malignant phenotypes of hepatoma cells were confirmed in vitro and in vivo. The regulatory mechanisms of DNMT3L were explored through MSP, western blot, and dual-luciferase assays. RESULTS: DNMT3L was found to be downregulated in HCC tissues and associated with better prognosis. Overexpression of DNMT3L inhibits cell proliferation and metastasis. Additionally, CDO1 was identified as a target gene of DNMT3L and also exhibits anti-cancer effects. DNMT3L upregulates CDO1 expression by competitively inhibiting DNMT3A-mediated methylation of CDO1 promoter. CONCLUSIONS: Our study revealed the role and epi-transcriptomic regulatory mechanism of DNMT3L in HCC, and underscored the essential role and applicability of big data analysis in elucidating complex biological processes.

Zinc-Bismuth Binary Alloy Enabling High-Performance Aqueous Zinc Ion Batteries.

Reconfiguration of zinc anodes efficiently mitigates dendrite formation and undesirable side reactions, thus favoring the long-term cycling performance of aqueous zinc ion batteries (AZIBs). This study synthesizes a Zn@Bi alloy anode (Zn@Bi) using the fusion method, and find that the anode surfaces synthesized using this method have an extremely high percentage of Zn(002) crystalline surfaces. Experimental results indicate that the addition of bismuth inhibits the hydrogen evolution reaction and corrosion of zinc anodes. The finite-element simulation results indicate that Zn@Bi can effectively achieve a uniform anodic electric field, thereby regulating the homogeneous depositions of zinc ions and reducing the production of Zn dendrite. Theoretical calculations reveal that the incorporation of Bi favors the anode structure stabilization and higher adsorption energy of Zn@Bi corresponds to better Zn deposition kinetics. The Zn@Bi//Zn@Bi symmetric cell demonstrates an extended cycle life of 1000 h. Furthermore, when pairing Zn@Bi with an α-MnO2 cathode to construct a Zn@Bi//MnO2 cell, a specific capacity of 119.3 mAh g-1 is maintained even after 1700 cycles at 1.2 A g-1 . This study sheds light on the development of dendrite-free anodes for advanced AZIBs.

Modal Decomposition of Acoustic Emissions from Pencil-Lead Breaks in an Isotropic Thin Plate.

Acoustic emission (AE) testing and Lamb wave inspection techniques have been widely used in non-destructive testing and structural health monitoring. For thin plates, the AEs arising from structural defect development (e.g., fatigue crack propagation) propagate as Lamb waves, and Lamb wave modes can be used to provide important information about the growth and localisation of defects. However, few sensors can be used to achieve the in situ wavenumber-frequency modal decomposition of AEs. This study explores the ability of a new multi-element piezoelectric sensor array to decompose AEs excited by pencil lead breaks (PLBs) on a thin isotropic plate. In this study, AEs were generated by out-of-plane (transverse) and in-plane (longitudinal) PLBs applied at the edge of the plate, and waveforms were recorded by both the new sensor array and a commercial AE sensor. Finite element analysis (FEA) simulations of PLBs were also conducted and the results were compared with the experimental results. To identify the wave modes present, the longitudinal and transverse PLB test results recorded by the new sensor array at five different plate locations were compared with FEA simulations using the same arrangement. Two-dimensional fast Fourier Transforms were then applied to the AE wavefields. It was found that the AE modal composition was dependent on the orientation of the PLB direction. The results suggest that this new sensor array can be used to identify the AE wave modes excited by PLBs in both in-plane and out-of-plane directions.

Fermentation process optimization, chemical analysis, and storage stability evaluation of a probiotic barley malt kvass.

Kvass is a popular low-alcohol beverage produced by the natural fermentation of dark rye bread or malt with complex microbial flora. However, few pieces of research focus on the microflora of traditional bread kvass, and the industrial kvass based on malt concentrate has some disadvantages, including the lack of viable probiotics and containing multiple artificial additives. Therefore, in the present study, based on the different homemade traditional bread kvass, the predominant species including Lacticaseibacillus paracasei, Acetobacter pasteurianus, and Saccharomyces cerevisiae were screened and identified. In addition, barley malt was used instead of bread for kvass production, and the co-fermentation conditions with three different strains were optimized as wort concentration of 7.4°Brix, cell ratio of 2/2/1 (S. cerevisiae/L. paracasei/A. pasteurianus), inoculum amount of 8%, fermentation temperature of 29.5 °C and fermentation time of 24.6 h. Moreover, the physicochemical (pH, total soluble solids, color, and alcohol content) and probiotic (microorganisms counting and antioxidant activity) properties of the barley malt kvass prepared at optimal conditions were symmetrically evaluated. Besides, compared with the commercial kvass products, the produced barley malt kvass exhibited better taste and more desirable antioxidant activity, and also maintained around 6-7 log CFU/mL of viable probiotic microorganisms during a week of storage. The present study not only enriched the biological resource of the traditional kvass, but also promoted the development of the kvass as a live-bacteria beverage.

Acoustic Emission Source Characterisation during Fatigue Crack Growth in Al 2024-T3 Specimens.

While acoustic emission (AE) testing can be used as a valuable technique in structural health monitoring and non-destructive testing, little research has been conducted to establish its sources, particularly in 2024-T3 aluminium alloys. The major contribution of this work is that it provides a method to obtain a better linear relationship of count rate with crack growth rate based on waveform. This paper aims to characterise AE sources by synchronising the AE waveforms with load levels and then to propose possible dominant frequency ranges. The AE waveforms during fatigue crack growth in edge-notched 2024-T3 aluminium specimens, from an initial crack length of 10 mm to 70 mm, were collected at two different load ratios R = 0.125 and 0.5. At the same time, the crack growth rate was determined using thermal imaging and associated control software. The AE waveforms obtained were processed using the fast Fourier transform. It was shown that a significantly higher AE count rate was recorded at R = 0.125 compared to R = 0.5 when the maximum load was kept the same. This means that the R-ratio would affect the total amount of AE activities collected. It was also found that the dominant frequency range of the AE waveforms directly related to crack growth was 152-487 kHz, and the ranges due to crack closure were likely to be 310 kHz-316 kHz and 500-700 kHz. Based on the proposed frequency ranges, waveform selection was conducted and a better linear relationship between count rate and crack growth rate was observed. This study provides a better understanding of the AE sources and waveforms for future structural health monitoring applications.

Regression-based heterogeneity analysis to identify overlapping subgroup structure in high-dimensional data.

Heterogeneity is a hallmark of complex diseases. Regression-based heterogeneity analysis, which is directly concerned with outcome-feature relationships, has led to a deeper understanding of disease biology. Such an analysis identifies the underlying subgroup structure and estimates the subgroup-specific regression coefficients. However, most of the existing regression-based heterogeneity analyses can only address disjoint subgroups; that is, each sample is assigned to only one subgroup. In reality, some samples have multiple labels, for example, many genes have several biological functions, and some cells of pure cell types transition into other types over time, which suggest that their outcome-feature relationships (regression coefficients) can be a mixture of relationships in more than one subgroups, and as a result, the disjoint subgrouping results can be unsatisfactory. To this end, we develop a novel approach to regression-based heterogeneity analysis, which takes into account possible overlaps between subgroups and high data dimensions. A subgroup membership vector is introduced for each sample, which is combined with a loss function. Considering the lack of information arising from small sample sizes, an l2$l_2$ norm penalty is developed for each membership vector to encourage similarity in its elements. A sparse penalization is also applied for regularized estimation and feature selection. Extensive simulations demonstrate its superiority over direct competitors. The analysis of Cancer Cell Line Encyclopedia data and lung cancer data from The Cancer Genome Atlas show that the proposed approach can identify an overlapping subgroup structure with favorable performance in prediction and stability.

Expression profiles of circular RNAs in colon biopsies from Crohn's disease patients by microarray analysis.

BACKGROUND: Circular RNAs (circRNAs) are involved in various diseases and serve as biomarkers. The present study aimed to investigate unique expression profiles of circRNAs in colon tissues of Crohn's disease (CD) and search novel biomarkers for the diagnosis. METHODS: Differentially expressed (DE) circRNAs in biopsies from four CD patients, four ulcerative colitis (UC) patients, and four healthy controls (HC) were screened by microarray. Hsa_circ_0062142 and hsa_circ_0001666 were verified in another expanded validation cohort. Bioinformatics analysis was applied to predict the function of two DE circRNAs. Receiver operating characteristic (ROC) curves were constructed to evaluate the diagnostic value of CD. RESULTS: The top 10 upregulated circRNAs in CD compared with HC were hsa_circ_0000691, hsa_circ_0001666, hsa_circ_0004183, hsa_circ_0009024, hsa_circ RNA_405324, hsa_circ_0002003, hsa_circ_0085323, hsa_circ_0040994, hsa_circ_0062142, and hsa_circ_0048148; the top 10 downregulated circRNAs were hsa_circ_0049356, hsa_circ RNA_405443, hsa_circ RNA_403556, hsa_circ_0092328, hsa_circ_0003979, hsa_circ_0074491, hsa_circ_0023461, hsa_circ RNA_406237, hsa_circ_0034044, and hsa_circ RNA_400564 (fold change in descending order). The expression levels of hsa_circ_0001666 and hsa_circ_0062142 in CD were significantly higher than those in UC and HC (p < 0.01). ROC curves suggested the favorable diagnostic value of hsa_circ_0062142 and hsa_circ_0001666 (AUC = 0.803 and 0.858, respectively, p < 0.01). In silico analysis indicated that these circRNAs may be involved in the progress of CD. CONCLUSION: Hsa_circ_0062142 and hsa_circ_0001666 may play critical roles in the pathogenesis and serve as potential biomarkers of CD.

Analysis of Factors Influencing Vibration Suppression of Spray Boom-Air Suspension for Medium and Small-Scale High-Clearance Sprayers.

Medium and small-scale high-clearance sprayers are widely applied in medium and small-scale farms. Owing to power and load limitations, it is difficult to manage the complex system for suppressing spray boom vibration. This study was conducted to design a spray boom-air suspension system suitable for medium and small-size high-clearance sprayers by combining spray boom vibration suppression and the characteristics of air spring charging/discharging. Thus, this study aims to address the non-homogeneous distribution of spray triggered by the spray boom vibrations in medium and small high-clearance sprayers. The effects of different elastic elements on the vibration suppression effect of the spray boom were compared. According to the bench test, the dynamic response results of the spray boom under transient and sinusoidal excitations indicate that air spring is more conducive to vibration suppression than coil spring. The results obtained from the field experiments indicate that under the low solid soil condition, the spray boom air suspension should match a small additional air chamber with a volume of approximately 0.6 L, and the damping coefficient of the damper should be approximately 1792 N·s/m. In the case of the high firm soil, the spray boom air suspension should match a large additional air chamber with a volume of approximately 3.6 L, while the damping coefficient of the damper should be set to approximately 1316 N·s/m. The soil with low moisture content and high firmness are unfavorable to the vibration suppression of the spray boom. This study provides a reference for enhancing the vibration suppression of the spray boom-air suspension and improving the spray uniformity of the sprayer.

Synthesis and evaluation of novel radioiodinated PSMA targeting ligands for potential radiotherapy of prostate cancer.

Radioligand therapy (RLT) using prostate-specific membrane antigen (PSMA) targeting ligands is an attractive option for the treatment of Prostate cancer (PCa) and its metastases. We report herein a series of radioiodinated glutamate-urea-lysine-phenylalanine derivatives as new PSMA ligands in which l-tyrosine and l-glutamic acid moieties were added to increase hydrophilicity concomitant with improvement of in vivo targeting properties. Compounds 8, 15, 19a/19b and 23a/23b were synthesized and radiolabeled with 125I by iododestannylation. All iodinated compounds displayed high binding affinities toward PSMA (IC50 = 1-13 nM). In vitro cell uptake studies demonstrated that compounds containing an l-tyrosine linker moiety (8, 15 and 19a/19b) showed higher internalization than MIP-1095 and 23a/23b, both without the l-tyrosine linker moiety. Biodistribution studies in mice bearing PC3-PIP and PC3 xenografts showed that [125I]8 and [125I]15 with higher lipophilicity exhibited higher nonspecific accumulations in the liver and intestinal tract, whereas [125I]19a/19b and [125I]23a/23b containing additional glutamic acid moieties showed higher accumulations in the kidney and implanted PC3-PIP (PSMA+) tumors. [125I]23b displayed a promising biodistribution profile with favorable tumor retention, fast clearance from the kidney, and 2-3-fold lower uptake in the liver and blood than that observed for [125I]MIP-1095. [125/131I]23b may serve as an optimal PSMA ligand for radiotherapy treatment of prostate cancer over-expressing PSMA.

An improved preparation of [18 F]AV-45 by simplified solid-phase extraction purification.

Amyvid (florbetapir f18, [18 F]AV-45, [18 F]5) was the first FDA-approved positron emission tomography imaging agent targeting ß-amyloid (Aß) plaques for assisting the diagnosis of Alzheimer disease. This work aimed to improve the [18 F]AV-45 ([18 F]5) preparation by using solid-phase extraction (SPE) purification. [18 F]AV-45 ([18 F]5) was synthesized by direct nucleophilic radiofluorination of O-tosylated precursor (1 mg) at 120°C in anhydrous dimethyl sulfoxide (DMSO), followed by acid hydrolysis of the N-Boc protecting group. Purification was accomplished by loading the crude reaction mixture to a cartridge (Oasis HLB 3 cc) and eluting with different combinations of solvents. This method removed the chemical impurity while leaving [18 F]AV-45 ([18 F]5) on the cartridge. The final dose was eluted by ethanol. [18 F]AV-45 ([18 F]5) was produced within 51 minutes (radiochemical yield 42.7 ± 5.9%, decay corrected, n = 3), and the radiochemical purity was greater than 95%. Total chemical impurity per batch (24.1 ± 2.7 µg per batch) was below the limit described in the package insert of Amyvid, florbetapir f18 (chemical mass: less than 50 µg/dose). In summary, [18 F]AV-45 ([18 F]5) was produced efficiently and reproducibly using a cartridge-based SPE purification. This method brings the process closer for routine preparation, similar to the commercially used [18 F]FDG.

Advanced RuO2 Thin Films for pH Sensing Application.

RuO2 thin films were prepared using magnetron sputtering under different deposition conditions, including direct current (DC) and radio frequency (RF) discharges, metallic/oxide cathodes, different substrate temperatures, pressures, and deposition times. The surface morphology, residual stress, composition, crystal structure, mechanical properties, and pH performances of these RuO2 thin films were investigated. The RuO2 thin films RF sputtered from a metallic cathode at 250 °C exhibited good pH sensitivity of 56.35 mV/pH. However, these films were rougher, less dense, and relatively softer. However, the DC sputtered RuO2 thin film prepared from an oxide cathode at 250 °C exhibited a pH sensitivity of 57.37 mV/pH with a smoother surface, denser microstructure and higher hardness. The thin film RF sputtered from the metallic cathode exhibited better pH response than those RF sputtered from the oxide cathode due to the higher percentage of the RuO3 phase present in this film.

In Vivo Ester Hydrolysis as a New Approach in Development of Positron Emission Tomography Tracers for Imaging Hypoxia.

Hypoxia is an important biochemical and physiological condition associated with uncontrolled growth of tumor. Measurement of hypoxia in tumor tissue may be useful in characterization of tumor progression and monitoring drug treatment. [18F]FMISO is the most widely employed radiotracer for imaging of hypoxic tissue with positron emission tomography (PET). However, it showed relatively low uptake in hypoxic tissues, which led to low target-to-background contrast in PET images. To overcome these shortcomings, two novel 2-fluoroproprioic acid esters, nitroimidazole derivatives 2-fluoropropionic acid 2-(2-nitro-imidazol-1-yl)-ethyl ester (FNPFT, [19F]5) and 2-fluoropropionic acid 2-(2-methyl-5-nitro-imidazol-1-yl)-ethyl ester (FMNPFT, [19F]8), were prepared and tested. Radiolabeling of [18F]5 and [18F]8 was accomplished in 45 min (radiochemical purity >95%, the decay-corrected radiochemical yield of [18F]5 was 11 ± 2%, and that of [18F]8 was 13 ± 2%, n = 5). In vitro cell uptake studies using EMT-6 tumor cells showed that both radiotracers [18F]5 and [18F]8 displayed significantly higher uptake in hypoxic cells than those under normoxic condition, while 2-[18F]fluoropropionic acid (2-[18F]FPA) displayed no difference. Biodistribution studies in mice bearing EMT-6 tumor showed that [18F]5, [18F]8, and 2-[18F]FPA displayed similar tumor and major organ uptakes. Tumor uptake values for all three agents were higher than those of [18F]FMISO, respectively ( P < 0.05). This is likely due to a rapid in vivo hydrolysis of [18F]5 and [18F]8 to their metabolite, 2-[18F]FPA. Micro PET imaging studies in the same EMT-6 implanted mice tumor model also demonstrated that both [18F]5 and [18F]8 displayed similar tumor uptake comparable to that of 2-[18F]FPA. In conclusion, two new fluorine-18 labeled nitroimidazole derivatives, [18F]5 and [18F]8, showed good tumor uptakes in mice bearing EMT-6 tumor. However, in vivo biodistribution results suggested that they were more likely reflect the predominance of in vivo produced metabolite, 2-[18F]FPA, which may not be related to tumor hypoxic condition.

Visual signal generation for the detection of influenza viruses by duplex recombinase polymerase amplification with lateral flow dipsticks.

We present a detailed study on visual detection of influenza viruses by duplex recombinase polymerase amplification (RPA) with lateral flow dipsticks (LFDs). The LFD consisted of two test lines and a control line, on which anti-fluorescein isothiocyanate antibodies, anti-digoxigenin antibodies, and biotinylated bovine serum albumin were immobilized, respectively. The performance of the LFD was evaluated with dual-labeled DNA amplicons. The results indicate that the detection of DNA amplicons by LFDs is specific and sensitive, with detection limits of 5.80 fmol for fluorescein isothiocyanate-labeled amplicons and 8.39 fmol for digoxigenin-labeled amplicons. We next developed a duplex RPA-LFD assay for simultaneous detection of influenza A virus and influenza B virus, and then optimized the parameters, including the reaction temperature, reaction time, and concentrations of primers and probes. Assessment of the specificity and sensitivity indicated that this assay is sensitive and specific for simultaneous detection of influenza viruses, with detection limits of 50 copies per reaction for influenza B virus and 500 copies per reaction for influenza A virus, without cross-reactivity with other pathogens. Compared with real-time PCR as a reference method to detect influenza viruses in clinical samples, the clinical sensitivity of the duplex RPA-LFD assay was 78.57% for influenza A virus and 87.50% for influenza B virus, with 100% specificity. In conclusion, the duplex RPA-LFD assay is a rapid, cost-effective, and sensitive method for the identification of influenza viruses.

Design and Investigation of Core/Shell GQDs/hMSN Nanoparticles as an Enhanced Drug Delivery Platform in Triple-Negative Breast Cancer.

Due to the excellent photoluminescent properties and singlet oxygen (1O2) generating efficiency, graphene quantum dots (GQDs) with maximal emission in near-infrared region (NIR) exhibited great potential in cancer imaging and therapy. However, GQDs can be cleared quickly via the renal system in vivo because of their ultrasmall size, which leads to the compromised cancer cell killing efficacy. Here, we report a hybrid nanoplatform, where GQDs were incorporated into the cavity of hollow mesoporous silica nanoparticles (hMSN) to form GQDs@hMSN-PEG nanoparticles (NPs). Optical characterization indicated that GQDs@hMSN-PEG NPs still maintained good absorption and emission properties from GQDs, and the composite NPs still possessed similar 1O2 generating efficiency. GQDs@hMSN-PEG NPs exhibited good biocompatibility in vitro and in vivo. High cargo-loading efficiency was achieved for doxorubicin (DOX), and the formed GQDs@hMSN(DOX)-PEG NPs showed the feasibility of tumor-oriented drug delivery. The extended retention time in tumor and good drug loading efficacy confirmed that GQDs@hMSN-PEG could serve as one promising candidate for combinational cancer treatment where photodynamic therapy and chemotherapy modules can be integrated into one system.

Reverse transcription recombinase polymerase amplification with lateral flow dipsticks for detection of influenza A virus and subtyping of H1 and H3.

Three reverse transcription recombinase polymerase amplification assays with lateral flow dipsticks (RT-RPA-LFD) were developed for identification of the matrix and hemagglutinin (HA) genes to detect influenza A virus and distinguish subtypes H1 and H3. Assessment of the assays' specificity showed that there was no cross-reactivity with other targets. Their limits of detection were 123.6 copies per reaction for the matrix gene, 677.1 copies per reaction for the H1 HA gene, and 112.2 copies/reaction for the H3 HA gene. Of 111 samples tested by RT-RPA-LFD assays, 27 were positive for influenza A virus, 14 were positive for H1, and 10 were positive for H3. Compared to the results obtained from real-time RT-PCR assays, the sensitivity of RT-RPA-LFD assays was 75%, 93.33% and 71.43% for the matrix, H1, and H3, with 100% specificity. The sensitivity of RT-RPA-LFD assays is lower than that of real-time RT-PCR, comparable or better than that of conventional RT-PCR, and much better than that of RIDTs. In conclusion, these assays offer an efficient and reliable tool for identification and subtyping of influenza A virus (subtype H1 and H3) in the resource-limited setting.

The chromosomal SezAT toxin-antitoxin system promotes the maintenance of the SsPI-1 pathogenicity island in epidemic Streptococcus suis.

Streptococcus suis has emerged as a causative agent of human meningitis and streptococcal toxic shock syndrome over the last years. The high pathogenicity of S. suis may be due in part to a laterally acquired pathogenicity island (renamed SsPI-1), which can spontaneously excise and transfer to recipients. Cells harboring excised SsPI-1 can potentially lose this island if cell division occurs prior to its reintegration; however, attempts to cure SsPI-1 from the host cells have been unsuccessful. Here, we report that an SsPI-1-borne Epsilon/Zeta toxin-antitoxin system (designated SezAT) promotes SsPI-1 stability in bacterial populations. The sezAT locus consists of two closely linked sezT and sezA genes encoding a toxin and its cognate antitoxin, respectively. Overproduction of SezT induces a bactericidal effect that can be neutralized by co-expression of SezA, but not by its later action. When devoid of a functional SezAT system, large-scale deletion of SsPI-1 is straightforward. Thus, SezAT serves to ensure inheritance of SsPI-1 during cell division, which may explain the persistence of epidemic S. suis. This report presents the first functional characterization of TA loci in S. suis, and the first biochemical evidence for the adaptive significance of the Epsilon/Zeta system in the evolution of pathogen virulence.

Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity.

BACKGROUND: Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. Shotgun sequencing method failed to complete the sequence of this genome. RESULTS: After persevering for 10 years and going over three generations of sequencing techniques, we successfully completed the sequence of the PaP1 genome with a length of 91,715 bp. Single-molecule real-time sequencing results revealed that this genome contains 51 N-6-methyladenines and 152 N-4-methylcytosines. Three significant modified sequence motifs were predicted, but not all of the sites found in the genome were methylated in these motifs. Further investigations revealed a novel immune mechanism of bacteria, in which host bacteria can recognise and repel modified bases containing inserts in a large scale. This mechanism could be accounted for the failure of the shotgun method in PaP1 genome sequencing. This problem was resolved using the nfi- mutant of Escherichia coli DH5α as a host bacterium to construct a shotgun library. CONCLUSIONS: This work provided insights into the hard-to-sequence phage PaP1 genome and discovered a new mechanism of bacterial immunity. The methylome of phage PaP1 is responsible for the failure of shotgun sequencing and for bacterial immunity mediated by enzyme Endo V activity; this methylome also provides a valuable resource for future studies on PaP1 genome replication and modification, as well as on gene regulation and host interaction.

A functional peptidoglycan hydrolase characterized from T4SS in 89K pathogenicity island of epidemic Streptococcus suis serotype 2.

BACKGROUND: Streptococcus suis serotype 2 (S. suis 2) has evolved efficient mechanisms to cause streptococcal toxic shock syndrome (STSS), which is a new emerging infectious disease linked to S. suis. We have previously reported that a type IV secretion system (T4SS) harbored by the specific 89K pathogenicity island (PAI) of S. suis 2 contributes to the development of STSS and mediates horizontal transfer of 89K. However, the 89K T4SS machinery assembly in vivo and in vitro is poorly understood, and the component acting directly to digest the bacterial cell wall needs to be identified. RESULTS: The virB1-89K gene product encoded in the 89K PAI is the only one that shows similarity to the Agrobacterium VirB1 component and contains a conserved CHAP domain that may function in peptidoglycan hydrolysis, which makes it a plausible candidate acting as a hydrolase against the peptidoglycan cell wall to allow the assembly of the T4SS apparatus. In the current study, the CHAP domain of VirB1-89K from S. suis 89K PAI was cloned and over-expressed in Escherichia coli, and its peptidoglycan-degrading activity in vitro was determined. The results indicated that the VirB1-89K CHAP domain can degrade the peptidoglycan layer of bacteria. Deletion of virB1-89K reduces significantly, but does not abolish, the virulence of S. suis in a mouse model. CONCLUSIONS: The experimental results presented here suggested that VirB1-89K facilitates the assembly of 89K T4SS apparatus by catalyzing the degradation of the peptidoglycan cell wall, thus contributing to the pathogenesis of S. suis 2 infection.

Synthesis of copper/carbon nanofibers by electrostatic spinning toward persulfate activation for treatment of antibiotic wastewater.

Antibiotics in water will cause serious harm to human health and ecosystem. Carbon-based materials and transition metals activated peroxodisulfate (PDS) to produce active species, which can degrade residual antibiotics in water. In this paper, Cu/CNF (carbon nanofibers) composites were first prepared by introducing Cu into CNF using electrostatic spinning technology, which was used to activate PDS to degrade tetracycline (TC). The degradation efficiency of Cu/CNF/PDS was 36.23% higher than that of CNF/PDS. The reason is that introducing Cu can increase the number of surface functional groups and specific surface area of CNF, and then improve the catalytic performance. The functional groups and Cu species are the active sites for catalytic PDS. Moreover, the main ways to degrade TC in the Cu/CNF/PDS system are singlet oxygen (1O2) and electron transfer. Based on the above analysis, we modified CNF with transition metal salts, prepared efficient environmental functional materials, and used them for PDS activation, providing a theoretical basis and technical support for the degradation of antibiotic pollutants and creating new ideas for other research.