Amplified nucleic acid sensing using programmed self-cleaving DNAzyme

A newly designed target-assisted self-cleavage (TASC) probe composed of a target-binding site and a DNAzyme domain undergoes TASC when activated via hybridization with a target DNA/RNA. This self-splicing or self-dissociation reaction occurs in a catalytic manner with the probe as a substrate and the target as a catalyst, since the fragmented products are automatically released from the target, thus amplifying the sequence information of the latter under non-PCR, i.e., isothermal and enzyme/reagent-free, conditions. A fluorescence-reporting TASC probe having a fluorescein/dabsyl FRET pair across the cleavage site allows a mix-and-read discrimination of single-nucleotide differences in the target.     

Evidence of DNA transfer through F-pilus channels during Escherichia coli conjugation

The mechanism of DNA transfer from Escherichia coli ( E. coli) Hfr donor strain AT2453 to recipient strain AB1157 during the conjugation process has been investigated by liquid atomic force microscopy (AFM). With the success of immobilizing both E. coli strains on gelatin-treated glass under aqueous solution, the F-pilus between an E. coli mating pair could be clearly imaged and dissected by an AFM probe. Another AFM probe functionalized with an anti-single-stranded DNA (ssDNA) antibody was then applied to detect transferring ssDNA. According to the AFM force spectrum, the transferring ssDNA could be detected only in the dissected area with a binding force of 109 +/- 5 pN measured. Our results provide direct evidence indicating that the DNA was transferred through the F-pilus channel between an E. coli mating pair during their conjugation.     

Sequences of E. coli O157:H7 detected by a PCR-acoustic wave sensor combination

In this paper, we report on the amplification by polymerase chain reaction (PCR) of a 509 base sequence unique to E. coli O157:H7. Immobilization of a probe for the bacterium on an acoustic wave sensor by the biotin-neutravidin interaction was employed to detect the on-line hybridization of the sequence with the sample obtained from PCR. The limit of detection was found to be 10(-8) M, which suggests that the method may be useful for detecting the organism in food, water and clinical samples. Finally, this approach lays the groundwork for incorporating the method into an integrated system for rapid PCR-based DNA analysis.     

Brightness through Local Constraint—LNA‐Enhanced FIT Hybridization Probes for In Vivo Ribonucleotide Particle Tracking

Imaging the dynamics of RNA in living cells is usually performed by means of transgenic approaches that require modification of RNA targets and cells. Fluorogenic hybridization probes would also allow the analysis of wild‐type organisms. We developed nuclease‐resistant DNA forced intercalation (FIT) probes that combine the high enhancement of fluorescence upon hybridization with the high brightness required to allow tracking of individual ribonucleotide particles (RNPs). In our design, a single thiazole orange (TO) intercalator dye is linked as a nucleobase surrogate and an adjacent locked nucleic acid (LNA) unit serves to introduce a local constraint. This closes fluorescence decay channels and thereby increases the brightness of the probe–target duplexes. As few as two probes were sufficient to enable the tracking of oskar mRNPs in wild‐type living Drosophila melanogaster oocytes.     

Protein photocrosslinking reveals dimer of dimers formation on MarR protein in Escherichia coli

The multiple antibiotic resistance regulatory protein(MarR) binds to two promoter sites on the marO operator in Escherichia coli.Our study showed that more than one MarR dimer proteins bound to either of its two promoter sites(Site I and Site II),suggesting that MarR might form higher complexes than homodimers when bound to DNA inside E.coli cells.To further verify this hypothesis,we site-specifically incorporated a photocrosslinking probe at the interface between two MarR dimer proteins.Photolysis in living E.coli cells revealed a covalent linkage between the two interdimer subunits of MarR,suggesting that MarR forms dimer of dimers in vivo.     

微量热法研究头孢菌素对大肠杆菌微生物活性的影响

用微量热法测定了两种头孢菌素头孢哌酮钠(CFZ)和头孢哌酮钠舒巴坦钠(CFZ-SBT)在37 ℃时对大肠杆菌DH5α代谢作用的影响. 根据产热曲线分别获得了大肠杆菌DH5α在不同浓度的头孢哌酮钠和头孢哌酮钠舒巴坦钠作用下的生长速率常数(k)、抑制率(I)、最大产热功率(Pm)以及最大产热功率所对应的时间tm等热动力学参数. 研究结果表明, 头孢哌酮钠和头孢哌酮钠舒巴坦钠对大肠杆菌的致死量分别为0.1和0.25 μg/mL. 通过研究k, I, Pm, tm和浓度(c)间的关系发现, 舒巴坦钠的加入没有增加头孢哌酮钠对大肠杆菌DH5α的抑制作用.     

Biosensor for the specific detection of a single viable B. anthracis spore

A simple membrane strip-based biosensor for the detection of viable B. anthracis spores was developed and combined with a spore germination procedure as well as a nucleic acid amplification reaction to identify as little as one viable B. anthracis spore in less than 12 h. The biosensor is based on identification of a unique mRNA sequence from the anthrax toxin activator (atxA) gene encoded on the toxin plasmid, pXO1. Preliminary work relied on plasmid vectors in both E. coli and B. thuringiensis expressing the atxA gene. Once the principle was firmly established, the vaccine strain of B. anthracis was used. After inducing germination and outgrowth of spores of B. anthracis (Sterne strain), RNA was extracted from lysed cells, amplified using nucleic acid sequence-based amplification (NASBA), and rapidly identified by the biosensor. While the biosensor assay requires only 15-min assay time, the overall process takes 12 h for the detection of as little as one viable B. anthracis spore, and is shortened significantly, if larger amounts of spores are present. The biosensor is based on an oligonucleotide sandwich-hybridization assay format. It uses a membrane flow-through system with an immobilized oligonucleotide probe that hybridizes with the target sequence. Signal amplification is provided when the target sequence hybridizes to a second oligonucleotide probe that has been coupled to dye-encapsulating liposomes. The dye in the liposomes then provides a signal that can be read visually or quantified with a hand-held reflectometer. The biosensor can detect as little as 1.5 fmol of target mRNA. Specificity analysis revealed no crossreactivity with closely related species such as B. cereus, B. megaterium, B. subtilis, B. thuringiensis etc.     

Quantitative changes in the elasticity and adhesive properties of Escherichia coli ZK1056 prey cells during predation by bdellovibrio bacteriovorus 109J

Atomic force microscopy (AFM) was used to explore the changes that occur in Escherichia coli ZK1056 prey cells while they are being consumed by the bacterial predator Bdellovibrio bacteriovorus 109J. Invaded prey cells, called bdelloplasts, undergo substantial chemical and physical changes that can be directly probed by AFM. In this work, we probe the elasticity and adhesive properties of uninvaded prey cells and bdelloplasts in a completely native state in dilute aqueous buffer without chemical fixation. Under these conditions, the rounded bdelloplasts were shown to be shorter than uninvaded prey cells. More interestingly, the extension portions of force curves taken on both kinds of cells clearly demonstrate that bdelloplasts are softer than uninvaded prey cells, reflecting a decrease in bdelloplast elasticity after invasion by Bdellovibrio predators. On average, the spring constant of uninvaded E. coli cells (0.23 +/- 0.02 N/m) was 3 times stiffer than that of the bdelloplast (0.064 +/- 0.001 N/m) when measured in a HEPES-metals buffer. The retraction portions of the force curves indicate that compared to uninvaded E. coli cells bdelloplasts adhere to the AFM tip with much larger pull-off forces but over comparable retraction distances. The strength of these adhesion forces decreases with increasing ionic strength, indicating that there is an electrostatic component to the adhesion events.     

Electrochemical detection of E. coli 16S rDNA sequence using air-plasma-activated fullerene-impregnated screen printed electrodes

A new DNA modified electrode for the electrochemical detection of 16S rDNA extracted from Escherichia coli (JCM1649) is proposed. The electrodes were fabricated by screen printing a fullerene-impregnated carbon ink onto a poly(methylmethacrylate) substrate and immobilizing a probe DNA on the surface after activating the electrode with air plasma. The results indicated a dramatic improvement in the surface coverage of the immobilized probe DNA, and of the reduction peak of the redox indicator (Co(phen)(3)(3+)) due to the incorporation of fullerene. By immobilizing the probe onto the fullerene-impregnated screen-printed electrodes, the PCR product of the 16S rDNA extracted from E. coli was directly detected without any pretreatment. A well defined signal difference was observed between the perfectly matching oligonucleotide and the mismatching one, and it was possible to detect the target at the modified electrode. This method enabled us to clearly detect the two base mismatches in the ca. 1500-bases long 16S rDNA sequence.     

Study of the bioeffects of CdTe quantum dots on Escherichia coli cells

Quantum dots (QDs) hold great potential for applications in nanomedicine, however, only a few studies investigate their toxic- and bio-effects. Using Escherichia coli (E. coli) cells as model, we found that CdTe QDs exhibited a dose-dependent inhibitory effect on cell growth by microcalorimetric technique and optical density (OD(600)). The growth rate constants (k) were determined, which showed that they were related to the concentration of QDs. The mechanism of cytotoxicity of QDs was also studied through the attenuated total reflection-fourier transform infrared (ATR-FTIR) spectra, fluorescence (FL) polarization, and scanning electron microscopy (SEM). It was clear that the cell out membrane was changed or damaged by the addition of QDs. Taken together, the results indicated that CdTe QDs have cytotoxic effects on E. coli cells, and this effects might attribute to the damaged structure of the cell out membrane, thus QDs and by-products (free radicals, reactive oxygen species (ROS), and free Cd(2+)) which might enter the cells.     

Isopentenyl diphosphate isomerase catalyzed reactions in D2O: product release limits the rate of this sluggish enzyme-catalyzed reaction

The E. coli isopentenyl diphosphate isomerase (IDI) catalyzed reaction of isopentenyl diphosphate (IPP) in D(2)O gives a 66% yield of dimethylallyl diphosphate labeled with deuterium at the (E)-methyl group (d-DMAPP) and a 34% yield of IPP labeled with 1 mol of deuterium at C-2 (d-IPP). This shows that the release to D(2)O of the initial product of the IDI-catalyzed reaction (d-DMAPP) is slower than its conversion to d-IPP. Product dissociation is therefore rate determining for isomerization of IPP with a rate constant k(dis) ≈ k(cat) = 0.08 s(-1). The data provide an estimated rate constant of k(as) = 6 × 10(3) M(-1) s(-1) for binding of DMAPP to E. coli IDI that is similar to rate constants determined for the binding of N-protonated 2-amino ethyl diphosphate intermediate analogs to IDI from yeast [Reardon, J. E.; Abeles, R. H. Biochemistry1986, 25, 5609-5616]. We propose that ligand binding to IDI is relatively slow because there is a significant kinetic barrier to reorganization of the initial encounter complex between enzyme, substrate, and an essential Mg(2+) to form the Michaelis complex where the metal cation bridges the protein and the substrate diphosphate group.     

Fabrication of microbial chip using collagen gel microstructure

A microbial chip was fabricated by filling the micropores on a glass substrate with collagen-embedded Escherichia coli(E. coli) cells, and characterized by scanning electrochemical microscopy (SECM) in a solution containing ferricyanide. The activity of the E. coli cells in the collagen gel microstructure was imaged and characterized with SECM by mapping the localized concentration of ferrocyanide produced by the respiration of the cells. The SECM-based activity measurement detected as low as approximately 100 E. coli cells. Furthermore, the optical-microscopic observation indicated that the E. coli cells on the chip proliferated during the incubation. The sequential SECM measurements were performed for the same E. coli chip to obtain the microbial growth curve for a small number of microorganisms.     

In Ssarch of new anti-bacterial target genes: a comparative/structural genomics approach

We outline a joint academic/industrial (CNRS/AVENTIS) functional genomics project aiming at the discovery of new anti-bacterial gene targets. Starting from all publicly available bacterial genomes, a subset of the most evolutionary conserved protein-coding genes has been identified. We retained genes with clear homolog in E. coli and at least one gram-positive bacterium among B.subtilis, M. tuberculosis, L. lactis or S. pyogenes. This subset was further reduced to genes encoding non-membrane proteins of unknown or hypothetical functions. The 221 E. coli Open Reading Frames (ORFs) identified through this comprehensive bioinformatic analysis are now submitted to a systematic 3-D structure determination protocol including cloning, protein expression and purification, crystallisation and X-ray diffraction. Our strategy was designed to focus on promising wide-spectrum targets as well as original biochemical pathways. Bioinformatics is used throughout all phases of project, including the initial large-scale comparative genomics analyses, the purification/expression and crystallisation stages for the detection of helpful sequence-specific features (e.g. cofactor binding motifs, non-structured N- or C- term extremities, etc ), and finally for the interpretation of the structures in conjunction with multiple sequence alignments for the identification of key residues, interaction areas on molecular surfaces, and overall function predictions.     

季铵盐型金属卟啉的合成及其对大肠杆菌生长代谢的抑制作用

以5,10,15,20-四(4′-吡啶基)卟啉为原料,合成了一系列季铵盐型金属卟啉1a,1b和2a～2c.使用LKB2277热活性监测器测定了大肠杆菌在不同浓度的金属卟啉1a,1b和2a～2c作用下的产热曲线,得到了大肠杆菌生长速率常数k,最大发热功率P_max和最大发热功率的出现时间t_p,发现季铵盐型金属卟啉2c对大肠杆菌生长代谢的抑制活性明显大于其它季铵盐型金属卟啉.     

Persistence length of wormlike micelles composed of ionic surfactants: self-consistent-field predictions

The persistence length of a wormlike micelle composed of ionic surfactants C(n)E(m)X(k) in an aqueous solvent is predicted by means of the self-consistent-field theory where C(n)E(m) is the conventional nonionic surfactant and X(k) is an additional sequence of k weakly charged (pH-dependent) segments. By considering a toroidal micelle at infinitesimal curvature, we evaluate the bending modulus of the wormlike micelle that corresponds to the total persistence length, consisting of an elastic/intrinsic and an electrostatic contribution. The total persistence length increases with pH and decreases with increasing background salt concentration. We estimate that the electrostatic persistence length l(p,e)(0) scales with respect to the Debye length kappa(-1) as l(p,e)(0) approximately kappa(-p) where p approximately 1.98 for wormlike micelles consisting of C(20)E(10)X(1) surfactants and p approximately 1.54 for wormlike micelles consisting of C(20)E(10)X(2) surfactants. The total persistence length l(p,t)(0) is a weak function of the head group length m but scales with the tail length n as l(p,t)(0) approximately n(x) where x approximately 2-2.6, depending on the corresponding head group length. Interestingly, l(p,t)(0) varies nonmonotonically with the number of charged groups k due to the opposing trends in the electrostatic and elastic bending rigidities upon variation of k.     

Photodynamic action of methylene blue: repair and mutation in Escherichia coli

The effects of the photodynamic action of methylene blue (MB-PDA) on strains of Escherichia coli were investigated to determine whether the dye could be used in photodynamic therapy (PDT). Using the method of alkaline sucrose gradient sedimentation, it was shown that in darkness MB induces a type of prelesion in DNA that transforms into single-strand breaks in alkaline conditions, provided that the dye is present during the processing of the gradient. This prelesion is completely reversible if the cells are washed immediately to remove the dye. However, after illumination with white light, the prelesions become "fixed" stable lesions, irreversible even after successive washings. The lethal damage induced by MB-PDA in E. coli can be repaired by the excision-repair system (about 30%) and by the recA-dependent repair system (about 70%). Polymerase I enzyme participates actively in the repair of the damage. MB-PDA is a weak mutagen and the induction of mutations by this treatment is restricted to high survival rates. Moreover, MB-PDA does not induce the SOS system (an inducible repair system dependent of the recA and loxA genes products), as measured by Weigle reactivation. However, it seems that this treatment can impair the repair systems in E. coli.     

Conditional glycosylation in eukaryotic cells using a biocompatible chemical inducer of dimerization

Chemical inducers of dimerization (CIDs) are cell-permeable small molecules capable of dimerizing two protein targets. The most widely used CID, the natural product rapamycin and its relatives, is immunosuppressive due to interactions with endogenous targets and thus has limited utility in vivo. Here we report a new biocompatible CID, Tmp-SLF, which dimerizes E. coli DHFR and FKBP and has no endogenous mammalian targets that would lead to unwanted in vivo side effects. We employed Tmp-SLF to modulate gene expression in a yeast three-hybrid assay. Finally, we engineered the Golgi-resident glycosyltransferase FucT7 for tunable control by Tmp-SLF in mammalian cells.     

生物热动力学研究——大肠杆菌生长速率和激活能

大肠杆菌生长的全热谱已被测定,再进一步根据其指数生长期的热谱信息,确定了它的生长速率和激活能。在指数生长期,细菌数按指数规律增加,可用下式表示:n_t=n_0e~(kt)(1)式中:t为指数生长期开始后的某一时间,n_0,n_t分别为指数生长期开始时和t时的细菌数,k为生长速率常数。因此,同期细菌输出的热功率也是按指数规律同步增长。可表示为:     

Probing chemical induced cellular stress by non-Faradaic electrochemical impedance spectroscopy using an Escherichia coli capacitive biochip

A new capacitive biochip was developed using carboxy-CNT activated gold interdigitated (GID) capacitors immobilized with E. coli cells for the detection of cellular stress caused by chemicals. Here, acetic acid, H(2)O(2) and NaCl were employed as model chemicals to test the biochip and monitored the responses under AC electrical field by non-Faradaic electrochemical impedance spectroscopy (nFEIS). The electrical properties of E. coli cells under different stresses were studied based on the change in surface capacitance as a function of applied frequency (300-600 MHz) in a label-free and noninvasive manner. The capacitive response of the E. coli biochip under normal conditions exhibited characteristic dispersion peaks at 463 and 582 MHz frequencies. Deformation of these signature peaks determined the toxicity of chemicals to E. coli on the capacitive biochip. The E. coli cells were sensitive to, and severely affected by 166-498 mM (1-3%) acetic acid with declined capacitance responses. The E. coli biochip exposed to H(2)O(2) exhibited adaptive responses at lower concentrations (<2%), while at a higher level (882 mM, 3%), the capacitance response declined due to oxidative toxicity in cells. However, E. coli cells were not severely affected by high NaCl levels (513-684 mM, 3-4%) as the cells tend to resist the salt stress. Our results demonstrated that the biochip response at a particular frequency enabled the determination of the severity of the stress imposed by chemicals and it can be potentially applied for monitoring unknown chemicals as an indicator of cytotoxicity.