Enzymatic Conversion of Flavonoids using Bacterial Chalcone Isomerase and Enoate Reductase

Flavonoids are a large group of plant secondary metabolites with a variety of biological properties and are therefore of interest to many scientists, as they can lead to industrially interesting intermediates. The anaerobic gut bacterium Eubacterium ramulus can catabolize flavonoids, but until now, the pathway has not been experimentally confirmed. In the present work, a chalcone isomerase (CHI) and an enoate reductase (ERED) could be identified through whole genome sequencing and gene motif search. These two enzymes were successfully cloned and expressed in Escherichia coli in their active form, even under aerobic conditions. The catabolic pathway of E. ramulus was confirmed by biotransformations of flavanones into dihydrochalcones. The engineered E. coli strain that expresses both enzymes was used for the conversion of several flavanones, underlining the applicability of this biocatalytic cascade reaction.     

A Parametric Study of Sample Lysis and DNA Purification Techniques for Use in Automated Devices

Abstract

We present a parametric study on the efficiency of several automatable procedures for the extraction and purification of DNA from a variety of pathogens. Based on the results of this work, an optimized protocol has been developed for use with both spiked buffers and nasal wash. All steps of this protocol are suitable for incorporation into a field-portable, automated sample preparation device. From introduction of the sample to elution of DNA, the entire process was completed in less than 60 min, and the time could be reduced further by automation. The recovered DNA is of sufficient quality for real-time or multiplex PCR amplification. The protocol was demonstrated on nasal wash samples spiked with E. coli containing the J7R and crmB genes. Subsequent testing on resequencing microarrays correctly identified the samples as Variola major virus.     

Models of virus capsids containing 72 pentameric capsomeres

A simple model for describing the non-quasi-equivalent icosahedral virus capsid composed of 72 pentameric capsomeres is developed. By means of six-step operations, a new 4-gons polyhedron P is obtained which contains 72 pentagons, 80 trigons and 210 quadrilaterals. More importantly, it bears icosahedral symmetry. The rationality of the existence of the 4-gons polyhedron P is further discussed. The results show that this model can be used to represent the capsids of papovaviruses.     

A Rapid and Sensitive Aptamer‐Based Electrochemical Biosensor for Direct Detection of Escherichia Coli O111

A sensitive and specific electrochemical biosensor based on target‐induced aptamer displacement was developed for direct detection of Escherichia coli O111. The aptamer for Escherichia coli O111 was immobilized on a gold electrode by hybridization with the capture probe anchored on the electrode surface through Au‐thiol binding. In the presence of Escherichia coli O111, the aptamer was dissociated from the capture probe‐aptamer duplex due to the stronger interaction between the aptamer and the Escherichia coli O111. The consequent single‐strand capture probe could be hybridized with biotinylated detection probe and tagged with streptavidin‐alkaline phosphatase, producing sensitive enzyme‐catalyzed electrochemical response to Escherichia coli O111. The designed biosensor showed weak electrochemical signal to Salmonella typhimurium, Staphylococcus aureus and common non‐pathogenic Escherichia coli, indicating high specificity for Escherichia coli O111. Under the optimal conditions, the proposed strategy could directly detect Escherichia coli O111 with the detection limit of 112 CFU mL^?1 in phosphate buffer saline and 305 CFU mL^?1 in milk within 3.5 h, demonstrated the sensitive and accurate quantification of target pathogenic bacteria. The designed biosensor could become a powerful tool for pathogenic microorganisms screening in clinical diagnostics, food safety, biothreat detection and environmental monitoring.     

Size‐selective purification of hepatitis B virus‐like particle in flow‐through chromatography: Types of ion exchange adsorbent and grafted polymer architecture

Hepatitis B virus‐like particles expressed in Escherichia coli were purified using anion exchange adsorbents grafted with polymer poly(oligo(ethylene glycol) methacrylate) in flow‐through chromatography mode. The virus‐like particles were selectively excluded, while the relatively smaller sized host cell proteins were absorbed. The exclusion of virus‐like particles was governed by the accessibility of binding sites (the size of adsorbents and the charge of grafted dextran chains) as well as the architecture (branch‐chain length) of the grafted polymer. The branch‐chain length of grafted polymer was altered by changing the type of monomers used. The larger adsorbent (90 μm) had an approximately twofold increase in the flow‐through recovery, as compared to the smaller adsorbent (30 μm). Generally, polymer‐grafted adsorbents improved the exclusion of the virus‐like particles. Overall, the middle branch‐chain length polymer grafted on larger adsorbent showed optimal performance at 92% flow‐through recovery with a purification factor of 1.53. A comparative study between the adsorbent with dextran grafts and the polymer‐grafted adsorbent showed that a better exclusion of virus‐like particles was achieved with the absorbent grafted with inert polymer. The grafted polymer was also shown to reduce strong interaction between binding sites and virus‐like particles, which preserved the particles’ structure.     

Combination of analytical and microbiological techniques to study the antimicrobial activity of a new active food packaging containing cinnamon or oregano against E. coli and S. aureus

The aim of this work is the optimization and application of a group of analytical and microbiological techniques in the study of the activity of essential oils (EOs) incorporated in a new antimicrobial packaging material and the research in depth of the interaction between the microbial cells and the individual compounds present in the active material. For this purpose the antimicrobial activity of the active packaging containing cinnamon or oregano was evaluated against E. coli and S. aureus. The vapour phase activity and the direct contact between the antimicrobial agents themselves, or once incorporated in the packaging material, and the microbial cells have been studied. The direct contact was studied using a broth dilution method. The vapour phase was evaluated by using a new method which involves the use of a filter disk containing the EOs. Furthermore, the kill time assay was used to determine the exposure time for the maximum efficiency in packaging, and transmission electron microscopy was used to investigate the antimicrobial activity and the possible mechanism of action against E. coli and S. aureus. Finally, the compounds absorbed by cells were identified. The results showed that the techniques used provide relevant information about the antibacterial activity of cinnamon and oregano in direct contact as well as in the vapour phase. The antimicrobial packaging showed a fast efficiency which supports its likely application as a food packaging material. Bacteria treated with EOs exhibit a wide range of significant abnormalities; these include formation of blebs, coagulation of cytoplasmatic constituents, collapse of the cell structure and lack of cytoplasmatic material. Some of these observations are correlated to the ability of some of these substances to disrupt envelop structure, especially the inner membrane. After an extraction from dead cells, cinnamaldehyde was detected by GC-MS in E. coli exposed to the active packaging containing cinnamon.     

Highly Sensitive Indicator‐Free Impedance Sensing of DNA Hybridization Based on Poly(m‐aminobenzenesulfonic acid)/TiO2 Nanosheet Membranes with Pulse Potentiostatic Method Preparation

A direct electrochemical detection procedure for DNA hybridization by using the electrochemical signal changes of conductive poly(m‐aminobenzenesulfonic) acid (PABSA)/TiO₂ nanosheet membranes, which were electropolymerized by using the pulse potentiostatic method, is reported. Due to the unique properties of TiO₂ nanoparticles, m‐aminobenzenesulfonic acid monomers tend to be adsorbed around the particles, and the electropolymerization efficiency is greatly improved. The combination of TiO₂ nanoparticles and PABSA resulted in a nanocomposite membrane with unique and novel nanosheet morphology that provides more activation sites and enhances the surface electron‐transfer rate. These characteristics were propitious for the magnification of PABSA electrochemical signals and the direct detection of DNA hybridization. Owing to the presence of abundant sulfonic acid groups, PABSA could overcome the drawbacks of polyaniline and be used to detect bioanalytes at physiological pH. DNA probes could be covalently attached to the sulfonic groups through the amines of DNA sequences by using an acyl chloride cross‐linking reaction. After immobilization of probe DNA, the electrochemical impedance value increased significantly compared to that of PABSA/TiO₂ nanosheet membranes, and then decreased dramatically after the hybridization reaction of the probe DNA with the complementary DNA sequence compared to that of the probe‐immobilized electrode. Electrochemical impedance spectroscopy was adopted for indicator‐free DNA biosensing, which had an eminent ability for the recognition between double‐base mismatched sequences or non‐complementary DNA sequences and complementary DNA sequences. A gene fragment, which is related to one of the screening genes for the transgenically modified plants, the cauliflower mosaic virus 35S gene was satisfactorily detected. This is the first report for the indicator‐free impedance DNA hybridization detection by using PABSA/TiO₂ membranes under neutral conditions.     

Primer Extension Reaction Assays for Incorporation of Deoxynucleotide Analogue into DNA

Incorporation of deoxynucleotide analogues into DNA is important for the expansion of DNA functions. Primer extension reactions are commonly used for the assay of such reaction events. However, current assay protocols generally rely on radiolabeling, fluorescence reporter labeling, or removal of specific deoxynucleotide triphosphate in the reaction mixture. Herein we report on the design of two novel assay protocols that utilize a dideoxynucleotide‐terminated template strand and a phosphorothiolate‐modified deoxynucleotide‐terminated template strand. We designed and synthesized a deoxyuridine triphosphate analogue (dU*TP) containing 2‐bromoisobutyryl group and demonstrated that it could be well recognized by ?29DNA polymerase, E. coli DNA polymerase I Klenow Fragment, Bst DNA polymerase Large Fragment, and E. coli DNA polymerase I Klenow Fragment (exo⁽), which translated to effective incorporation of dU*TP into DNA. dU*TP was also successfully incorporated into extremely long single‐stranded DNA at high‐density using ?29 DNA polymerase by rolling circle amplification.     

Chitosan‐capped sulfur microparticles grafted on UV‐treated PET surface

Antimicrobial materials with immobilized particles are of considerable interest. Sulfur, as one of the abundant elements on earth, is cheap and environmentally friendly; therefore, sulfur particles (SPs) can be used as an effective, nontoxic and low‐cost alternative to metal particles. SPs were prepared by precipitation method using sodium thiosulfate and hydrochloric acid in the presence of chitosan as a stabilizer. Further, SPs were grafted on polyethylene terephthalate (PET) foil activated by ultraviolet radiation. The changes in surface properties of modified foils were characterized by contact angle measurement, electrokinetic analysis and X‐ray photoelectron spectroscopy (XPS). The contact angle decreased on the UV‐treated sample, owing to the formation of oxidized groups. The presence of nitrogen and sulfur on the polymer surface, revealed by XPS, showed that chitosan‐capped SPs were bound to this surface. The surface morphology of samples and particle sizes were examined by scanning electron microscopy. The size of SPs increased after grafting on surface to a few micrometres. The antibacterial activity of the PET samples was tested against Staphylococcus epidermidis and Escherichia coli bacteria strains. UV‐treated samples grafted with one of the tested chitosan‐capped SPs demonstrated antibacterial effect against both of the bacteria strains. This new nanocomposite has potential to be used in medical applications as an antibacterial agent or in food processing as an antimicrobial food packaging material. Food spoilage caused by microorganisms such as E. coli during distribution and storage has a major impact on food quality and shelf life.     

DNA polymerase I-mediated repair of 365 nm-induced single-strand breaks in the DNA of Escherichia coli.

Abstract. Irradiation of closed circular phage Λ DNA in vivo at 365 nm results in the induction of single-strand breaks and alkali-labile lesions at rates of 1.1 × 10^-14, and 0.2 × 10^-14/dalton/J/m², respectively. The sum of the induction rates is similar to the rate of induction of single-strand breaks plus alkali-labile lesions (1 × 10^-14/dalton/J/m²) observed in the E. coli genome. Postirradiation incubation of wild-type cells in buffer results in rapid repair of the breaks (up to 80% repaired in 10 min). No repair was observed in a DNA polymerase I-deficient mutant of E. coli.     

Rapid and sensitive DNA target detection using enzyme amplified electrochemical detection based on microchip

A rapid and sensitive DNA targets detection using enzyme amplified electrochemical detection (ED) based on microchip was described. We employed a biotin‐modified DNA, which reacted with avidin‐conjugated horseradish peroxidase (avidin–HRP) to obtain the HRP‐labeled DNA probe and hybridized with its complementary target. After hybridization, the mixture containing dsDNA‐HRP, excess ssDNA‐HRP, and remaining avidin–HRP was separated by MCE. The separations were performed at a separation voltage of +1.6 kV and were completed in less than 100 s. The HRP was used as catalytic labels to catalyze H₂O₂/o‐aminophenol reaction. Target DNA could be detected by the HRP‐catalyzed reduction with ED. With this protocol, the limits of quantification for the hybridization assay of 21‐ and 39‐mer DNA fragments were of 8×10^?12 M and 1.2×10^?11 M, respectively. The proposed method has been applied satisfactorily in the analysis of Escherichia coli genomic DNA. We selected the detection of PCR amplifications from the gene of E. coli to test the real applicability of our method. By using an asymmetric PCR protocol, we obtained ssDNA targets of 148 bp that could be directly hybridized by the single‐stranded probe and detected with ED.     

Absence of repair replication following ultraviolet irradiation of an excision-deficient mutant of Escherichia coli

The excision -repair of damaged DNA in bacteria and other systems probably requires at least three enzymes to carry out the following steps in sequence: (1) Recognition of a structural distortion in the DNA and the production of an endonucleolytic cleavage of the damaged strand near the lesion. (2) The simultaneous peeling back of the damaged strand and resynthesis of the excised region, with eventual cleavage of the damaged segment from the DNA. (3) The rejoining of the newly synthesized strand to contiguous parental DNA. Evidence for all three steps has been obtained from in vivo studies. The E. coli DNA polymerase has been shown to carry out step # 2 in vitro [1] and the polynucleotide ligase has the required specificity for step # 3[2–4]. An enzyme responsible for step # 1 has been purified from Micrococcus lysodeikticus [5,6] but not from E. coli, although a class of u.v. sensitive mutants in E. coli has been shown to be defective in this step in the repair sequence. In such mutants the release of pyrimidine dimers from the damaged DNA is not observed during post-irradiation growth of u.v. irradiated cultures [7]. It would be predicted, as a consequence, that the next step, non-conservative repair replication, would not be seen in these mutants. Hanawalt and Petti-john showed this to be true for the double mutant E. coli B_8-1 that includes a deficiency in dimer excision [8]. In the present study we have looked more closely at an E. coli K-12 strain that has only the uvrA6 deficiency that results in inability to excise pyrimidine dimers.     

PHOTOLESIONS AND BIOLOGICAL INACTIVATION OF PLASMID DNA ON 254 nm IRRADIATION AND COMPARISON WITH 193 nm LASER IRRADIATION

Plasmid pTZ18R and calf thymus DNA in aerated neutral aqueous solution were irradiated by continuous 254 nm light. The quantum yields are φ_ssb= 4.0 × 10^-5 and φ_dsb= 1.4 × 10^-6 for single- and double-strand break formation, respectively, φ_br= 2.3 × 10^-5 for base release, φ_dn= 2.1 × 10^-3 for destruction of nucleotides, and φ_icl×φ_lds× 1 × 10^-6 for interstrand cross-links and locally denatured sites, respectively. The presence of Tris-HCI/ ethylenediaminetetraacetic acid (10:1, pH 7.5) buffer strongly reduces φ_ssb, The corresponding φ values, obtained on employing pulsed 193 nm laser irradiation, are much larger than those using λ_irr, = 254 nm. This is ascribed to a contribution of chemical reactions induced by photoionization, which is absent for 254 nm irradiation. The quantum yields of inactivation of plasmid DNA (λ_irr= 254 nm) were measured by transformation of the Escherichia coli strains AB1157 (wild type), φ_ina(1157) = 1.6 × 10^-4, AB1886 (uvr^-), φ_ina(1886) = 4.2 × 10^-4, AB2463 (rec^-), φ_ina(2463) = 4.1 × 10^-4 and AB2480 (uvr^- rec^-), φ_ina(2480) = 3.1 × 10^-3. The quantum yields of inactivation of plasmid DNA are compared with those of the four E. coli strains (denoted as chromosomal DNA inactivation) obtained from the literature. The results for E. coli strain AB2480 show that the chromosomal DNA and the plasmid DNA are both inactivated by a single pyrimidine photodimer per genome. With the E. coli strain AB2463 inactivation of plasmid and chromosomal DNA is the same for the same total damage per genome and is ～ 10 times smaller than for AB2480. This is explained by photodimer repair in chromosomal and plasmid DNA and by the absence of dsb repair in both cases. In the repair wild-type strain AB1157, inactivation of the plasmid DNA is roughly 100 times higher than that of the chromosomal DNA. We postulate that a portion of this difference is due to repair of dsb by the recA system in chromosomal DNA and that such repair does not take place in the plasmid DNA. The biological results from 254 nm irradiation are compared with those from 193 nm laser irradiation.     

Activation of Nanoparticles by Biosorption for <Emphasis Type="Italic">E. coli</Emphasis> Detection in Milk and Apple Juice

Two types of silver nanoparticles were activated by specific sorption of biomolecules for the detection of Escherichia coli. The capture of this bacterium was performed using polyclonal antibodies (anti-E. coli) biosorbed onto nanospheres or nanorice through a protein-A layer. The bacterial detection was achieved using surface enhancement Raman scattering in order to compare the performance of these two nanoparticles. The activated silver nanospheres showed a better performance mainly due to the dimension of these nanoparticles. The detection limit has been established using the automated Raman mapping system. The technique was capable of detecting 10³ cells/mL in milk and apple juice without any pre-enrichment. With an overall assay time less than 1 h, the process could be easily adapted to detect other pathogens by selecting the pertinent antibody. Furthermore, PCR was used for the DNA verification to assess whether the selected bacterial strain was identical before and after detection.     

Antibacterial cellulose acetate films incorporated with N‐halamine‐modified nano‐crystalline cellulose particles

Cellulose acetate (CA) membranes have been widely used as food packaging materials as well as reverse osmosis systems. This study presents the manufacturing of composite CA film with antibacterial properties which is essential for CA film applications in the industry. N‐Halamine precursor of polymethacrylamide‐modified nano‐crystalline cellulose particles (NCC‐PMAMs) were prepared and incorporated into CA film. The composite films with intercalated structure were formed via a solvent‐casting technique. After chlorination, the composite film CA/NCC‐PMAM‐Cl‐1.0 with 1.82 × 10¹⁶ atoms/cm² covalently bonded chlorine showed excellent antibacterial properties by inactivating 6.04 logs of Staphylococcus aureus and 6.27 logs of Escherichia coli within 10 and 5 min, respectively. According to X‐ray diffraction spectra, NCC‐PMAMs behaved as a facilitator for film crystallization. The mechanical strength of the composite film also increased compared with that of pure CA film. However, the composite film became brittle and the maximum decomposition temperature decreased slightly. Preliminary data of in vitro cytocompatibility evaluation indicate that the film is not toxic and has potential use in food packaging. Copyright © 2016 John Wiley & Sons, Ltd.     

Modelling of sorbic acid diffusion through bacterial cellulose-based antimicrobial films

Antimicrobial packaging protects the product from the external environment and microbial contamination, conferring numerous advantages on human health. Interest in biopolymers as packaging materials has considerably increased recently. Bacterial cellulose is an interesting biomaterial produced as nanofibrils by Acetobacter xylinium and is a promising candidate due to its remarkable properties. New composite materials with antimicrobial properties were developed in this work, containing poly(vinyl alcohol) (PVA) as polymer matrix and ground bacterial cellulose (BC) as reinforcing fibres. Sorbic acid was used as an antimicrobial agent because it is a preservative recognised in the food industry. The materials obtained were studied using Fourier-transformed infrared spectroscopy (FTIR). The swelling rate of the composites was also measured. Release experiments of sorbic acid from the composite films into water were performed and the mass transfer phenomena were investigated using Fick’s law of diffusion. The antimicrobial effect was tested against Escherichia coli K12-MG1655. The results obtained indicated that the new biocomposite films could be promising antimicrobial food packaging materials.     

A Multi-component All-DNA Biosensing System Controlled by a DNAzyme

We report on a programmable all-DNA biosensing system that centers on the use of a 4-way junction (4WJ) to transduce a DNAzyme reaction into an amplified signal output. A target acts as a primary input to activate an RNA-cleaving DNAzyme, which then cleaves an RNA-containing DNA substrate that is designed to be a component of a 4WJ. The formation of the 4WJ controls the release of a DNA output that becomes an input to initiate catalytic hairpin assembly (CHA), which produces a second DNA output that controls assembly of a split G-quadruplex as a fluorescence signal generator. The 4WJ can be configured to produce either a turn-off or turn-on switch to control the degree of CHA, allowing target concentration to be determined in a quantitative manner. We demonstrate this approach by creating a sensor for E. coli that could detect as low as 50 E. coli cells mL⁻¹ within 85 min and offers an amplified bacterial detection method that does not require a protein enzyme.     

Development of a novel approach for the production of dried genomic DNA for use as standards for qualitative PCR testing of food-borne pathogens

As part of a multi-centre European project, FOOD-PCR, the feasibility of a novel approach for production of dried bacterial DNA that could be used as certified reference materials (CRM) was assessed. Selected strains of Salmonella typhimurium, Listeria monocytogenes, Escherichia coli O157, Campylobacter jejuni and Yersinia enterocolitica were used to produce genomic DNA (gDNA). These preparations gave support to method development for qualitative polymerase chain reaction (PCR) detection methods for food-borne pathogens. Purified gDNA was transformed into stable and dry gDNA by using polypropylene vials as carrier and applying a vacuum-drying technique. The gDNA preparations were shown to be sufficiently stable under ambient transport conditions without cooling and proved to have long-term stability at 5°C of at least 22 months. The dried DNA was easily reconstituted by addition of distilled water then gentle shaking. These studies have shown that production of stable and dry bacterial gDNA material is feasible and could help satisfy the increasing need for certified reference DNA positive control samples in the field of PCR testing for detection and verification of food-borne microbial pathogens.