Interspecies Horizontal Transfer and Specific Integration of the Mosquitocidal Toxin-Encoding Plasmid pTAND672-2 from Bacillus thuringiensis subsp. israelensis to Lysinibacillus sphaericus.

pTAND672-2, a 144-kb resident plasmid of Bacillus thuringiensis serovar israelensis strain TAND672, was sequenced and characterized. This extrachromosomal element carries mosquitocidal toxin-, conjugation-, and recombinase-encoding genes, together with a putative arbitrium system, a genetic module recently discovered in temperate phages controlling lysogeny-lysis transition and in mobile genetic elements (MGEs) where its function remains clarified. Using conjugation experiments, pTAND672-2 is shown to be a novel integrative and conjugative element (ICE), which can horizontally transfer from B. thuringiensis serovar israelensis to Lysinibacillus sphaericus, another mosquitocidal bacterium, where it integrates into the chromosome. Its integration and circularization are reversible and involve a single-cross recombination between 33-bp specific sites, attB in the chromosome of L. sphaericus and attP in pTAND672-2. CDS143, coding for the putative tyrosine integrase Int143 distantly related to site-specific tyrosine Xer recombinases and phage integrases, can mediate the integration of pTAND672-2 to attB. The B. thuringiensis mosquito-killing genes carried by pTAND672-2 are efficiently transcribed and expressed in L. sphaericus, displaying a slight increased toxicity in this bacterium against Aedes albopictus larvae. The occurrence of pTAND672-2-like plasmids within the Bacillus cereus group was also explored and indicated that they all share a similar genetic backbone with diverse plasmid sizes, ranging from 58 to 225 kb. Interestingly, among them, the pEFR-4-4 plasmid of Bacillus paranthracis EFR-4 and p5 of B. thuringiensis BT-59 also display conjugative capability; moreover, like pTAND672-2 displays a chimeric structure between the pCH_133-e- and pBtoxis-like plasmids, pBTHD789-3 also appears to be mosaic of two plasmids. IMPORTANCE Horizontal transfer of mobile genetic elements carrying mosquitocidal toxin genes may play a driving role in the diversity of mosquitocidal bacteria. Here, the 144-kb mosquitocidal toxin-encoding plasmid pTAND672-2 is the first verified integrative and conjugative element (ICE) identified in Bacillus thuringiensis serovar israelensis. The key tyrosine integrase Int143, involved in the specific integration, is distantly related to other tyrosine recombinases. The study also reports the occurrence and potential interspecies transmission of pTAND672-2-like plasmids with varied sizes in B. thuringiensis, Bacillus paranthracis, and Bacillus wiedmannii isolates belonging to the Bacillus cereus group. This study is important for further understanding the evolution and ecology of mosquitocidal bacteria, as well as for providing new direction for the genetic engineering of biopesticides in the control of disease-transmitting mosquitoes.

MSFF-CDCGAN: A novel method to predict RNA secondary structure based on Generative Adversarial Network.

Access to RNA secondary structure is a prerequisite for understanding and mastering RNA function. RNA secondary structures play an important role in cells, they can cause or contribute to neurological disorders and can be applied in the medical field. However, the experimental method to obtain RNA secondary structure is costly, laborious and not universal. Although computational methods can predict RNA secondary structure more accurately for short-sequence RNAs, it cannot predict long-sequence RNAs and pseudoknot, which is the bottleneck of RNA secondary structure prediction at present. In recent years, researchers have attempted to use deep learning algorithms to predict RNA secondary structure and have achieved results. However, the small amount of data on the secondary structure of long-sequence RNAs leads to the low accuracy of deep learning methods to predict the secondary structure of RNAs across races. Similarly, RNA structure with pseudoknot is very complex and insufficient data caused the deep learning algorithm to struggle to predict the secondary structure of RNA containing pseudoknots. The RNA data are encoded into grayscale images by a unique encoding method based on the real RNA secondary structure and sequence information. Then, this paper reasonably expands the image data to increase the amount of RNA data, solves the problem of insufficient data for predicting long sequences and RNA secondary structure with pseudoknots in current deep learning methods, and provides a good data foundation for deep learning.The article proposes a multi-scale feature fusion Conditional Deep Convolutional Generative Adversarial Network prediction model (MSFF-CDCGAN) based on the improved Conditional Deep Convolutional Generative Adversarial Network (CDCGAN) model to predict RNA secondary structure. The experimental results showed that the MSFF-CDCGAN model could predict long-sequence RNAs and pseudoknots more accurately than traditional prediction methods. This paper introduces Generative Adversarial Network (GAN) to RNA secondary structure prediction for the first time. It uses a unique image encoding approach to expand the original RNA data set, thus transforming the structure prediction problem into an image analysis problem and effectively solving the bottleneck in RNA secondary structure prediction.

Land-Ocean Exchange Mechanism of Chlorinated Paraffins and Polycyclic Aromatic Hydrocarbons with Diverse Sources in a Coastal Zone Boundary Area, North China: The Role of Regional Atmospheric Transmission.

The marine environment is regarded as a crucial "sink" of numerous land-origin pollutants. As typical boundary regions, the coastal and offshore areas are used to evaluate the dominating transfer process and land-ocean exchange mechanism of semivolatile organic compounds. In air samples collected from a coastal area in North China over a whole year, chlorinated paraffins (CPs), including short-chain CPs and medium-chain CPs, and prior control 16 polycyclic aromatic hydrocarbons (PAHs) were determined, with mean concentrations of 25.8 and 94.7 ng/m3, respectively. Results of different gas-particle partitioning models indicated that the steady-state hypothesis provides a better description of the possible land-ocean exchange molecular mechanism. The source-sink influences for CPs and PAHs were affected by the predominant atmospheric motion, which alternated between gaseous diffusion and particulate sedimentation in different seasons. Source apportionment results indicated that different transfer characteristics contributed to the source divergence of ambient CPs and PAHs within 12 nautical miles in the same area. Coal/biomass combustion and diesel/natural gas combustion were the main PAH sources in the coast site (43.1%) and sea site (35.3%), respectively. Similar industrial sources CP-52 and CP-42 were the main CP sources in the coast site (41.4%) and sea site (40.8%), respectively.

Dependence of water adsorption on the surface structure of silicon wafers aged under different environmental conditions.

Most materials exposed to ambient air can adsorb water molecules and the adsorption capability strongly depends on the surface property. The water contact angle has been widely used as a measure for surface wettability; however, a question can still be asked whether the water contact angle can be used as an adequate sole predictor for water adsorption on the surface in humid air. In this paper, HF-etched silicon wafers were aged (oxidized) under different environmental conditions at room temperature to grow surface layers with varying water contact angles from ∼0° (fully hydrophilic) to ∼83° (highly hydrophobic), and water adsorption as a function of relative humidity (RH) was studied on such surfaces. The thickness and structure of the adsorbed water layer were found to depend on not only the surface wettability on each surface, but also the history of surface oxidation conditions. In particular, the silicon wafer surface oxidized in liquid water uptakes significantly more water from humid air than the fully-hydroxylated native oxide surface (SiOx/OH), even though its water contact angle is higher than that on the SiOx/OH surface. This could be attributed to the formation of a gel-like structure during oxidation in liquid water.

Screening antitumor bioactive fraction from Sauromatum giganteum (Engl.) Cusimano & Hett and sensitive cell lines with the serum pharmacology method and identification by UPLC-TOF-MS.

Sauromatum giganteum (Engl.) Cusimano & Hett Tuber are used in Chinese folklore medicine for treatment of neoplasms. However, the claim has not been scientifically validated. The aim of the study is to screen the antitumor bioactive fraction of Sauromatum giganteum (Engl.) Cusimano & Hett Tuber and sensitive tumor cell lines using a cytotoxicity assay in vitro and tumor transplantation method in vivo, to support its use in folk medicine. The petroleum ether fraction, chloroform fraction, ethyl acetate fraction, n-butanol fraction and water fraction were successively extracted by turn by the maceration under reflux assay. Screening of antitumor bioactive fraction and sensitive cell lines were measured by MTT assay and the serum pharmacology method, and in vivo the antitumor activities of the active fraction was evaluated by using S180 or H22 tumor-bearing mice model and Kunming mice. The active constituents of ethyl acetate fraction of Sauromatum giganteum (Engl.) Cusimano & Hett were characterized by UPLC-TOF-MS. Compared with control groups, mice serum containing ethyl acetate fraction had a inhibition effect on SMMC-7721 cell, SGC-7901 cell, MCF-7 cell, HeLa cell, A549 cell, HT-29, and MDA-MB-231, respectively, but mice serum containing other four fractions had no different with that of control group. The inhibition capabilities of mice serum containing ethyl acetate fraction on the seven cell lines in descending order is SGC-7901 > SMMC-7721 > MCF-7 > HT-29 > A549 > HeLa > MDA-MB-231. In vivo the inhibition rate of 106, 318, 954 mg/kg·d ethyl acetate fraction dry extract to sarcoma S180 is 15.22%, 26.15% and 40.24%, respectively, and life prolonging rate to hepatoma H22 is 33.61%, 40.16% and 55.74%. A total of 14 compounds were identified in the ethyl acetate fraction of Sauromatum giganteum (Engl.) Cusimano & Hett. The results of the experimental studies proved the antitumor activity of Sauromatum giganteum (Engl.) Cusimano & Hett and supported the traditional use of this plant. These data indicate the potential for the use of ethyl acetate fraction of Sauromatum giganteum (Engl.) Cusimano & Hett Tuber in tumor therapy, anti-tumor activity on cancer cell line in descending order is SGC-7901 > SMMC-7721 > MCF-7 > HT-29 > A549 > HeLa > MDA-MB-231.

Europium Nanoparticle-Based Lateral Flow Strip Biosensors for the Detection of Quinoxaline Antibiotics and Their Main Metabolites in Fish Feeds and Tissues.

Olaquindox (OLA) and quinocetone (QCT) have been prohibited in aquatic products due to their significant toxicity and side effects. In this study, rapid and visual europium nanoparticle (EuNP)-based lateral flow strip biosensors (LFSBs) were developed for the simultaneous quantitative detection of OLA, QCT, and 3-methyl-quinoxaline-2-carboxylic acid (MQCA) in fish feed and tissue. The EuNP-LFSBs enabled sensitive detection for OLA, QCT, and MQCA with a limit of detection of 0.067, 0.017, and 0.099 ng/mL (R2 ≥ 0.9776) within 10 min. The average recovery of the EuNP-LFSBs was 95.13%, and relative standard deviations were below 9.38%. The method was verified by high-performance liquid chromatography (HPLC), and the test results were consistent. Therefore, the proposed LFSBs serve as a powerful tool to monitor quinoxalines in fish feeds and their residues in fish tissues.

Advances in Aptamer-Based Conjugate Recognition Techniques for the Detection of Small Molecules in Food.

Small molecules are significant risk factors for causing food safety issues, posing serious threats to human health. Sensitive screening for hazards is beneficial for enhancing public security. However, traditional detection methods are unable to meet the requirements for the field screening of small molecules. Therefore, it is necessary to develop applicable methods with high levels of sensitivity and specificity to identify the small molecules. Aptamers are short-chain nucleic acids that can specifically bind to small molecules. By utilizing aptamers to enhance the performance of recognition technology, it is possible to achieve high selectivity and sensitivity levels when detecting small molecules. There have been several varieties of aptamer target recognition techniques developed to improve the ability to detect small molecules in recent years. This review focuses on the principles of detection platforms, classifies the conjugating methods between small molecules and aptamers, summarizes advancements in aptamer-based conjugate recognition techniques for the detection of small molecules in food, and seeks to provide emerging powerful tools in the field of point-of-care diagnostics.

Development of a loop-mediated isothermal amplification assay for detection of Cronobacter spp. (Enterobacter sakazakii).

Contamination of Cronobacter spp. (Enterobacter sakazakii) in infant formulas and other food products is a severe problem. Here a loop-mediated isothermal amplification (LAMP) assay was developed for rapidly detecting Cronobacter spp. in powdered infant formula. Sequences of 16S/23S rDNA internal intergenic spacer of Cronobacter spp. were used as the target template to design LAMP primers. The detection outcome can be evaluated by the white precipitate or the fluorescence intensity under ultraviolet irradiation, both visible to naked eyes. The sensitivity and specificity of the LAMP assay was further analyzed in comparison with that of regular PCR and real time quantitative PCR. The results showed that all of Cronobacter spp. strains display positive reaction to the detections while all of the non-Cronobacter spp. strains were negative, and that the LAMP assay exhibits a high sensitivity of 9.1 fg/µL (The sensitivity of regular PCR and real time quantitative PCR is 91 and 9.1 pg/µL, respectively.). The amplified reaction could be accomplished in about 1 h, with the results visible to naked eyes. Hence, the LAMP assay developed by this study can provide a rapid and simple approach for the detection of Cronobacter spp. in infant formula.

Influence of the Phagemid PfNC7401 on Cereulide-Producing Bacillus cereus NC7401.

A phagemid-cured strain, NC7401-∆Pf, was constructed to survey the biological function of the plasmidal prophage PfNC7401 in cereulide-producing Bacillus cereus NC7401. The transcriptome analysis between the mutant and the wild strains revealed a series of differentially expressed genes mainly involved in different function classifications, including the two-component signal transduction system, bacterial structure, transporters, related antibiotic response, purine biosynthesis, non-ribosomal peptide synthetases (NRPS) and related secondary metabolites, and aromatic or other amino acid synthesis. BIOLOG and phenotypic experiment analyses confirmed that PfNC7401 may affect phage immunity and the metabolism of several amino acids, including L-Alanine, which was suggested to be related to one precursor (D-Alanine) of cereulide synthesis. However, neither the transcription levels of the cereulide production-related genes (e.g., ilvB, cesA, cesB, and cesH) nor the cereulide production nor cell cytotoxicity were affected by the presence or absence of PfNC7401, corresponding with the transcriptome data, in which only four genes unrelated to cereulide synthesis on the plasmid-carrying ces gene cluster were affected by the curing of PfNC7401.

Ethanol but not aqueous extracts of tubers of Sauromatum Giganteum(Engl.) Cusimano and Hett inhibit cancer cell proliferation.

BACKGROUND: Both alcohol and aqueous extracts of Sauromatum giganteum(Engl.) Cusimano and Hett, the dried root tuber of which is named Baifuzi in Chinese, have been used for folklore treatment of cancer in Northeast of China. However, little is known about which is most suitable to the cancer therapy. MATERIALS AND METHODS: Serum pharmacology and MTT assays were adopted to detect the effects of ethanol and aqueous extracts of Sauromatum giganteum(Engl.) Cusimano and Hett , prepared by heat reflux methods, on proliferation of different cancer cells. RESULTS: Cancer cells treated with medium supplemented with 10%, 20%, 40% serum(v/v) containing ethanol extract had a decline in viability, with inhibition rates of 7.69%, 21.8%, 41.9% in MCF-7 cells, 42.8%, 48.1%, 51.8% in SGC-7901 cells, 44.1%, 49.2%, 53.7% in SMMC-7721 cells, 6.8%, 15.2%, 39.8% in HepG2 cells, 7.57%, 16.3%, 36.2% in HeLa cells, 6.24%, 12.5%, 27.4% in A549 cells, and 7.20%, 17.5%, 31.3% in MDA-MB-231 cells, respectively. Viability in the aqueous extract groups was no different with that of controls. CONCLUSIONS: An ethanol extract of Sauromatum giganteum(Engl.) Cusimano and Hett inhibited the proliferation of SMMC-7721, SGC-7901 and MCF-7 cells, which supports the use of alcoholic but not aqueous extracts for control of sensive cancers, which might include hepatocarcinoma, gastric cancer and breast cancer.

[Colloidal gold immunochromatographic strip for rapid detection of melamine].

To develop a specific, rapid, and convenient immunochromatography assay (ICA) to detect melamine residues in dairy products and feed sample. Colloidal gold particles labeled with purified monoclonal antibody against anti-melamine were used as the detector reagent. The MEL-OVA (the conjugate of melamine and ovalbumin) and goat anti-mouse melamine IgG were blotted on the test and control regions of nitrocellulose membrane. The strip was then assembled with sample pad, absorbing pad, and dorsal shield. The limit of detection (LOD) is 50 microg/L. The test trip was applied to detect melamine in milk, milk powder, and animal feeds, with detection limits of 100 microg/L for milk, 100 ng/g for milk powder, 200 ng/g for feeds. Compared to LC-MS/MS, the ICA could be used to screen a large number of dairy products and feed samples for melamine residue.