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The vibration signal of rolling bearing is usually complex and the useful fault information is hidden in the background noise, therefore, it is a challenge to identify rolling bearing faults from the complex vibration environment. In this paper, a novel multilayer deep learning convolutional neural network (CNN) method to identify rolling bearing fault is proposed. Firstly, in order to avoid the influence of different characteristics of the input data on the identification accuracy, a normalization preprocessing method is applied to preprocess the vibration signals of rolling bearings. Secondly, a multilayer CNN based on deep learning is designed in this paper to improve the fault identification accuracy of rolling bearing. Simulation data and experimental data analysis results show that the proposed method has better performance than SVM method and ANN method without any manual feature extractor design. [ABSTRACT FROM AUTHOR]

The progressive development of amplified DNA sensors using nucleic acid-based machineries, involving the isothermal autonomous synthesis of the Mg2+-dependent DNAzyme, is used for the amplified, multiplexed analysis of genes (Smallpox, TP53) and metal ions (Ag+, Hg2+). The DNA sensing machineries are based on the assembly of two sensing modules consisting of two nucleic add scaffolds that indude recognition sites for the two genes and replication tracks that yield the nicking domains for NtBbvCI and two different Mg2+-dependent DNAzyme sequences. In the presence of any of the genes or the genes together, their binding to the respective recognition sequences triggers the nicking/polymerization machineries, leading to the synthesis of two different Mg2+-dependent DNAzyme sequences. The cleavage of two different fluorophore/quencher-modified substrates by the respective DNAzymes leads to the fluorescence of F1 and/or F2 as readout signals for the detection of the genes. The detection limits for analyzing the Smallpox and TPS3 genes correspond to 0.1 nM Similarly, two different nucleic add scaffolds that indude Ag+-ions or Hg2+-ions recognition sequences and the replication tracks that yield the NtBbvCI nicking domains and the respective Mg2+-dependent DNAzyme sequences are implemented as niddng/replication machineries for the amplified, multiplexed analysis of the two ions, with detection limits corresponding to 1 nM. The ions sensing modules reveal selectivities dominated by the respective recognition sequences associated with the scaffolds. [ABSTRACT FROM AUTHOR]

The article focuses on approaches in DNA nanostructures for activation of catalytic DNA cascades and use of the DNA nanostructures for control in reaction, sensing, logic operations, and assembly of complex nanostructures. Topics discussed include formation of DNA nanostructures by the autonomous hybridization chain reaction (HCR), use of catalytic nucleic acids DNAzymes in designing of logic gate systems and activation of catalytic cascade by coupling reaction of DNAzymes.

The amplified, highly sensitive detection of DNA using the dendritic rolling circle amplification (RCA) is introduced. The analytical platform includes a circular DNA and a structurally tailored hairpin structure. The circular nucleic acid template includes a recognition sequence for the analyte DNA (the Tay-Sachs mutant gene), a complementary sequence to the Mg2+-dependent DNAzyme, and a sequence identical to the loop region of the coadded hairpin structure. The functional hairpin in the system consists of the analyte-sequence that is caged in the stem region and a single-stranded loop domain that communicates with the RCA product. The analyte activates the RCA process, leading to DNA chains consisting of the Mg2+-dependent DNAzyme and sequences that are complementary to the loop of the functional hairpin structure. Opening of the coadded hairpin releases the caged analyte sequence, resulting in the dendritic RCA-induced synthesis of the Mg2+-dependent DNAzyme units. The DNAzyme-catalyzed cleavage of a fluorophore/quencher-modified substrate leads to a fluorescence readout signal. The method enabled the analysis of the target DNA with a detection limit corresponding to 1 aM. By the design of two different circular DNAs that include recognition sites for two different target genes, complementary sequences for two different Mg2+-dependent DNAzyme sequences and two different functional hairpin structures, the dendritic RCA-stimulated multiplexed analysis of two different genes is demonstrated. The amplified dendritic RCA detection of DNA is further implemented to yield the hemin/G-quadruplex horseradish peroxidase (HRP)-mimicking DNAzyme as catalytic labels that provide colorimetric or chemiluminescent readout signals. [ABSTRACT FROM AUTHOR]

The progressive development of amplified DNA sensors and aptasensors using replication/nicking enzymes/DNAzyme machineries is described. The sensing platforms are based on the tailoring of a DNA template on which the recognition of the target DNA or the formation of the aptamer-substrate complex trigger on the autonomous isothermal replication/nicking processes and the displacement of a Mg2+-dependent DNAzyme that catalyzes the generation of a fluorophore-labeled nucleic acid acting as readout signal for the analyses. Three different DNA sensing configurations are described, where in the ultimate configuration the target sequence is incorporated into a nucleic acid blocker structure associated with the sensing template. The target-triggered isothermal autonomous replication/nicking process on the modified template results in the formation of the Mg2+-dependent DNAzyme tethered to a free strand consisting of the target sequence. This activates additional template units for the nucleic acid self-replication process, resulting in the ultrasensitive detection of the target DNA (detection limit 1 aM). Similarly, amplified aptamer-based sensing platforms for cocaine are developed along these concepts. The modification of the cocaine-detection template by the addition of a nucleic acid sequence that enables the autonomous secondary coupled activation of a polymerization/nicking machinery and DNAzyme generation path leads to an improved analysis of cocaine (detection limit 10 nM). [ABSTRACT FROM AUTHOR]

Hybrid systems consisting of nucleic-acid-functionalized silver nanoclusters (AgNCs) and graphene oxide (GO) are used for the development of fluorescent DNA sensors and aptasensors, and for the multiplexed analysis of a series of genes of infectious pathogens. Two types of nucleic-acid-stabilized AgNCs are used: one type includes the red-emitting AgNCs (616 nm) and the second type is near-infrared-emitting AgNCs (775 nm). Whereas the nucleic-acid-stabilized AgNCs do not bind to GO, the conjugation of single-stranded nucleic acid to the DNA-stabilized AgNCs leads to the adsorption of the hybrid nanostructures to GO and to the fluorescence quenching of the AgNCs. By the conjugation of oligonucleotide sequences acting as probes for target genes, or as aptamer sequences, to the nucleic-acid-protected AgNCs, the desorption of the probe/nucleic-acid-stabilized AgNCs from GO through the formation of duplex DNA structures or aptamer–substrate complexes leads to the generation of fluorescence as a readout signal for the sensing events. The hybrid nanostructures are implemented for the analysis of hepatitis B virus gene (HBV), the immunodeficiency virus gene (HIV), and the syphilis (Treponema pallidum) gene. Multiplexed analysis of the genes is demonstrated. The nucleic-acid-AgNCs-modified GO is also applied to detect ATP or thrombin through the release of the respective AgNCs-labeled aptamer–substrate complexes from GO. [ABSTRACT FROM AUTHOR]

The Zn2+-dependent ligation DNAzyme is implemented as a biocatalyst for the amplified detection of a target DNA by the autonomous replication of a nucleic acid reporter unit that is generated by the catalyzed ligation process. The reporter units enhance the formation of active DNAzyme units, thus leading to the isothermal auto-catalytic formation of the reporter elements. The system was further developed and applied for the amplified detection of Tay-Sachs genetic disorder mutant, with a detection limit of 1.0 × 10-11 M. Besides providing a versatile paradigm for the amplified detection of DNA, the system reveals a new, enzyme-free, isothermal, autocatalytic mechanism that introduces means for effective programmed synthesis. [ABSTRACT FROM AUTHOR]

An enzyme-free amplified detection platform is described using the horseradish peroxidase (HRP)-mimicking DNAzyme as an amplifying label. Two hairpin structures that include three-fourths and one-fourth of the HRP-mimicking DNAzyme in caged, inactive configurations are used as functional elements for the amplified detection of the target DNA. In the presence of the analyte DNA, one of the hairpins is opened, and this triggers the autonomous cross-opening of the two hairpins using the strand displacement principle. This leads to the formation of nanowires consisting of the HRP-mimicking DNAzyme. The resulting DNA nanowires act as catalytic labels for the colorimetric or chemiluminescent readout of the sensing processes (the term "enzyme-free" refers to a protein-free catalyst). The analytical platform allows the sensing of the analyte DNA with a detection limit corresponding to 1 x 10-13 M. The optimized system acts as a versatile sensing platform, and by coaddition of a "helper" hairpin structure any DNA sequence may be analyzed by the system. This is exemplified with the detection of the BRCA1 oncogene with a detection limit of 1 x 10-13 M. [ABSTRACT FROM AUTHOR]

A layer-by-layer film composed of DNA and inorganic zirconium ion (Zr 4+) was fabricated on the surface of gold thin film, and an electric field triggered disintegration of the multilayer film was studied by using electrochemical surface plasmon resonance (EC-SPR). EC-SPR results demonstrated that the film was disassembled upon the application of an electric field and the disassembly rate varied with the applied potential, leading to the controlled release of DNA. The electrodissolution could be switched off by removing the electric potential and reactivated by reapplying the potential. By incorporating plasmid DNA (pDNA) in to this controlled release system, the multilayer film could sustain the consecutive release of pDNA electrochemically. The released pDNA retained its integrity and transfection activity, and expressed enhanced green fluorescent protein (EGFP) after being transfected into HEK 293 cells. The electrochemical systems, with advantages of miniaturization, surface-tailoring, safety, simplicity, convenience, automation, low-cost, and free of immune reactions, made the electrical route a very attractive gene-delivery alternative. [ABSTRACT FROM AUTHOR]

The sensing of pathogen infection and subsequent triggering of innate immunity are key to controlling zoonotic infections. Myxoma virus (MV) is a cytoplasmic DNA poxvirus that in nature infects only rabbits. Our previous studies have shown that MV infection of primary mouse cells is restricted by virus-induced type I interferon (IFN). However, little is known about the innate sensor(s) involved in activating signaling pathways leading to cellular defense responses in primary human immune cells. Here, we show that the complete restriction of MV infection in the primary human fibroblasts requires both tumor necrosis factor (TNF) and type I IFN. We also demonstrate that MV infection of primary human macrophages (pHMs) activates the cytoplasmic RNA sensor called retinoic acid inducible gene I (RIG-I), which coordinately induces the production of both TNF and type I IFN. Of note, RIG-I sensing of MV infection in pHMs initiates a sustained TNF induction through the sequential involvement of the downstream IFN-regulatory factors 3 and 7 (IRF3 and IRF7). Thus, RIG-I-mediated co-induction of TNF and type I IFN by virus-infected pHMs represents a novel innate defense mechanism to restrict viral infection in human cells. These results also reveal a new regulatory mechanism for TNF induction following viral infection. [ABSTRACT FROM AUTHOR]

A systematic study of the amplified optical detection of DNA by Mg2+-dependent DNAzyme subunits is described. The use of two DNAzyme subunits and the respective fluorophore/quencher-modified substrate allows the detection of the target DNA with a sensitivity corresponding to 1 × 10-9 M. The use of two functional hairpin structures that include the DNAzyme subunits in a caged, inactive configuration leads, in the presence of the target DNA, to the opening of one of the hairpins and to the activation of an autonomous cross-opening process of the two hairpins, which affords polymer DNA wires consisting of the Mg2+-dependent DNAzyme subunits. This amplification paradigm leads to the analysis of the target DNA with a sensitivity corresponding to 1 × 10-14 M. The amplification mixture composed of the two hairpins can be implemented as a versatile sensing platform for analyzing any gene in the presence of the appropriate hairpin probe. This is exemplified with the detection of the BRCA1 oncogene. [ABSTRACT FROM AUTHOR]

Mouse embryo fibroblasts (MEFs) are a widely used cell culture system in life sciences, including virology. Here, we show that although primary MEFs are nonpermissive to myxoma virus replication, the corresponding immortalized MEFs support a highly productive myxoma virus infection. We further demonstrate that this permissive phenotype for myxoma virus in immortalized MEFs is due to the immortalization-associated selective block to the cellular alpha/beta interferon induction machinery involved in responding to myxoma virus challenge. Thus, our report presents a clear example, illustrating that a drastic phenotypic alteration can occur with respect to virus infection between primary cells and their immortalized counterparts. [ABSTRACT FROM AUTHOR]

Twodifferent methods to self-assemble red- or yellow-luminescentnucleic acids-stabilized Ag nanoclusters (NCs) nanowires are presented.By one method, the autonomous hybridization–polymerizationprocess between two nucleic acids leads to polymer chains consistingof sequence-specific loops for the stabilization of the red- or yellow-emittingAg NCs. By the other method, the nucleic acid-triggered hybridizationchain reaction (HCR) involving the cross-opening of two functionalhairpins leads to sequence-specific DNA loops and a nucleic acid scaffoldthat stabilize the respective red- or yellow-emitting Ag NCs. Themicrometer-long luminescent Ag NC-functionalized nanowires are imagedby AFM and confocal microscopy. [ABSTRACT FROM AUTHOR]

The fluorescent dyes methylene blue, MB+, and thionine, Th+, can be trapped in the pores of mesoporous silica, MP-Si02, by means of functional nanostructures consisting of the Mg2+- or Zn2+-dependent DNAzyme sequences. In the presence of Mg2+ or Zn2+ ions the respective DNAzymes are activated, leading to the specific cleavage of the respective caps, and the selective release of MB+ or Th+. The enlargement of the conserved loop domains of the Mg2+- or Zn2+-dependent DNAzyme sequences with foreign nucleotides prohibits the formation of active DNAzymes and eliminates the release of the respective dyes. This is due to the flexibility of the loops that lacks affinity for the association of the ions. The insertion of aptamer sequences (e.g., the adenosine-5'-triphosphate (ATP) aptamer) or ion-binding sequences (e.g., T-rich Hg2+ ion-binding domains) as foreign components to the loop regions allows the formation of active Mg2+- or Zn2+-dependent DNAzyme structures through the cooperative formation of aptamer-ATP complexes or T-Hg2+-T bridges. These aptamer--substrate complexes or T-Hg2+-T bridges allosterically stabilize and activate the DNAzymes, thus allowing the selective release of the fluorescent substrates MB+ or Th+. The metal ion-driven DNAzyme release of substrates from the pores of MP-SiO and particularly the allosteric activation of the DNAzymes through cooperative aptamer--substrate complexes or metalion bridges, has important future nanomedical implications for targeted release of drugs. This is demonstrated with the triggered release of the anticancer drug, doxorubicin, by the Mg2+-DNAzyme-locked pores or by the aptamer-ATP complex-triggered activation of the Mg2+-dependent DNAzyme. [ABSTRACT FROM AUTHOR]

Biological systems that are capable of performing computational operations could be of use in bioengineering and nanomedicine, and DNA and other biomolecules have already been used as active components in biocomputational circuits. There have also been demonstrations of DNA/RNA-enzyme-based automatons, logic control of gene expression, and RNA systems for processing of intracellular information. However, for biocomputational circuits to be useful for applications it will be necessary to develop a library of computing elements, to demonstrate the modular coupling of these elements, and to demonstrate that this approach is scalable. Here, we report the construction of a DNA-based computational platform that uses a library of catalytic nucleic acids (DNAzymes), and their substrates, for the input-guided dynamic assembly of a universal set of logic gates and a half-adder/half-subtractor system. We demonstrate multilayered gate cascades, fan-out gates and parallel logic gate operations. In response to input markers, the system can regulate the controlled expression of anti-sense molecules, or aptamers, that act as inhibitors for enzymes. [ABSTRACT FROM AUTHOR]

The authors have recently demonstrated that wild-type myxoma virus (MV) tagged with gfp (vMyxgfp) can generate a tumor-specific infection that productively infects and clears human tumor-derived xenografts when injected intratumorly into human gliomas transplanted into immunodeficient mice (Lun et al, 2005). To expand the understanding of MV tropism in cancer cells from a specific tissue lineage, the authors have screened a series of human glioma cells (U87, U118, U251, U343, U373) for myxoma virus replication and oncolysis. To assess the viral tropism determinants for these infections, the authors have screened myxoma virus knockout constructs that have been deleted for specific host range genes (M-T2, M-T4, M-T5, M11L, and M063), as well as a control MV gene knockout construct with no known host range function (vMyx135KO) but is highly attenuated in rabbits. The authors report wide variation in the ability of various vMyx-hrKOs to replicate and spread in the human glioma cells as measured by early and late viral gene expression. This differential ability to support vMyx-hrKO productive viral replication is consistent with levels of endogenous activated Akt in the various gliomas. The authors have identified one vMyx-hrKO virus (vMyx63KO) and one nonhost range knockout construct (vMyx135KO) that appear to replicate in the gliomas even more efficiently than the wild-type virus and that reduce the viability of the infected gliomas. These knockout viruses also inhibit the proliferation of gliomas in a manner similar to the wild-type virus. Together these data, as well as the fact that these knockout viruses are attenuated in their natural hosts, may represent environmentally safer candidate oncolytic viruses for usage in human trials. [ABSTRACT FROM AUTHOR]

There are five hot springs named separately SHANGT, ZHONGT, WENT, XIAT and SHENT in Lushan County, Pingdingshan City, Henan Province. The archaeal diversity of the five hot springs was investigated and analyzed. 16S rDNA v4-5 genes of arehaea were sequenced by lllumina Hisiq2500 PE250 technolog). The numbers of sample sequences and OTUs were sorted by using Uparse, Mothur, SILVA, MUSCLE and Qiime software. Finally, the archaeal abundance and diversity in the five hot springs were analyzed. 87 993, 67 326, 44 400, 48 611 and 48 495 effective reads have been obtained from SHANCT, ZHONCT, WENT, XIAT and SHENT respectively, and 520, 280, 678,451 and 437 OTUs have been acquired. The analysis of archaeal classification showed that the arehaea from the five hot springs could be classified into 11 phyla, in which Thaumarchaeota accounted for 95. 25% and was the dominant arehaea. In the genera level, the dominant arehaea of the SHANGT, ZHONGT and WENT was Candidalus-Nilrosocaldus, and unidentified-Thaumarchaeota was the dominant arehaea in XIAT and SHENT. The results showed that the five hot springs in Lushan are rich in microbial resources. The research provided basic data for further research and utilization of the arehaea resources in the five hot springs of Lushan. [ABSTRACT FROM AUTHOR]

Myxoma virus (MV) encodes a cell surface protein (M135R) that is predicted to mimic the host alpha/beta interferon receptor (IFN-α/β-R) and thus prevent IFN-α/β from triggering a host antiviral response. This prediction is based on sequence similarity to B18R, the viral IFN-α/β-R from vaccinia virus (VV), which has been demonstrated to bind and inhibit type I interferons. However, M135R is only half the size of VV B18R. All other poxvirus-encoded IFN-α/β-R homologs align only to the amino-terminal half of M135R. Peptide antibodies raised against M135R were used for immunoblotting and immunofluorescence and indicate that M135R is expressed as an early gene and that the product is a cell surface N-linked glycoprotein that is not secreted. In contrast to the predicted properties of M135R as an inhibitor of type I interferon, all binding and inhibition assays designed to demonstrate whether M135R can interact with IFN-α/β have been negative. However, pathogenesis studies with a targeted M135-knockout MV construct (vMyx135KO) indicate that the deletion of M135R severely attenuates MV pathogenesis in the European rabbit. We propose that M135R is an important immunomodulatory virulence factor for myxomatosis but that the target immune ligand is not from the predicted type I interferon family and remains to be identified. [ABSTRACT FROM AUTHOR]

Supramolecular organized multilayers were constructed by multiwalled carbon nanotubes modified with ferrocene-derivatized poly(allylamine) redox polymer and glucose oxidase by electrostatic self-assembly. From the analysis of voltammetric signals and fluorescence results, a linear increment of the coverage of enzyme per bilayer was estimated, which demonstrated that the multilayer is constructed in a spatially ordered manner. The cyclic voltammograms obtained from the indium tin oxide (ITO) electrodes coated by the (Fc-PAHCNT/GOx)nmultilayers revealed that bioelectrocatalytic response is directly correlated to the number of deposited bilayers; that is, the sensitivity is tunable by controlling the number of bilayers associated with ITO electrodes. The incorporation of redox-polymer-functionalized carbon nanotubes (CNT) into enzyme films resulted in a 6−10-fold increase in the glucose electrocatalytic current; the bimolecular rate constant of FADH2oxidation (wiring efficiency) was increased up to 12-fold. Impedance spectroscopy data have yielded the electron diffusion coefficient (De) of this nanostructure to be over 10-8cm2s-1, which is typically higher than those systems without CNT by at least a factor of 10, indicating that electron transport in the new supramolecular architecture was enhanced by communication of the redox active site of enzyme, redox polymer, and CNT. [ABSTRACT FROM AUTHOR]

To meet the requirement of surface plasmon resonance (SPR) sensing, controlling the thickness of the gold film is very important. Here, we report an efficient and simple approach to prepare a SPR-active substrate when the thickness of the gold film is larger than the optimizing 50 nm and smaller than 100 nm. This method is based on anodic electrodissolution of gold in electrolyte containing chloride ions. Using this method, the thickness of gold films can be easily changed at a nanometer scale by controlling the number of potential scans and the concentrations of chloride ions in the electrolyte. At the same time, the influence of gold film thickness on the SPR signal is recorded by SPR in real time. To assess the change of the surface roughness and morphology of gold flint through anodic electrodissolution, atomic force microscopy was used. The surface roughness of the same Au film before and after anodic electrodissolution is 1.179 and 2.767 nm, respectively. The change of the surface roughness of Au film brings out a slight angle shift of SPR. This indicates that surface electrodissolution of the gold does not affect the character of the original bulk film and this film can be used for SPR experiments. To confirm our expectation, a simple adsorption experiment of cytochrome c (Cyt c) on the gold film treated with anodic electrodissolution modified by 11-mercaptoundecanic acid was carried out. The angle shift of SPR confirmed the adsorption of Cyt c, and the cyclic voltammetry of Cyt c provided a complementary confirmation for the adsorption of Cyt c. These results show that this approach provides a good way to change the thicker gold film to an optimized thickness of SPR sensing. The great advantage brought by this approach is in that it can convert the waste gold films with greater thicknesses fabricated by the vacuum deposition method or other methods into useful materials as active SPR substrates. [ABSTRACT FROM AUTHOR]

Subversion or appropriation of cellular signal transduction pathways is a common strategy employed by viruses to promote an environment within infected cells that supports the viral replicative cycle. Using subsets of 3T3 murine fibroblasts previously shown to differ in their ability to support myxoma virus (MV) replication, we investigated the role of host serine-threonine kinases (STKs) as potential mediators of the permissive phenotype. Both permissive and nonpermissive 3T3 cells supported equivalent levels of virion binding, entry, and early virus gene expression, indicating that MV tropism in 3T3 cells was not determined by receptormediated entry. In contrast, late virus gene expression and viral DNA replication were selectively compromised in restrictive 3T3 cells. Addition of specific protein kinase inhibitors, many of which shared the ability to influence the activity of the STKs p21-activated kinase 1 (PAK-1) and Raf-1 attenuated MV replication in permissive 3T3 cells. Western blot detection of the phosphorylated forms of PAK-1 (Thr423) and Raf-1 (Ser338) confirmed activation of these kinases in permissive cells after MV infection or gamma interferon treatment, but the activated forms of both kinases were greatly reduced or absent in restrictive 3T3 cells. The biological significance of these activations was demonstrated by using the autoinhibitory domain of PAK-1 (amino acids 83 to 149), expression of which reduced the efficiency of MV infection in permissive 3T3 cells concurrent with a decrease in PAK-1 activation. In comparison, overexpression of a constitutively active PAK-1 (T423E) mutant increased MV replication in restrictive 3T3 cells. These observations suggest that induced signaling via cellular STKs may play important roles in determining the permissiveness of host cells to poxvirus infection. [ABSTRACT FROM AUTHOR]