Design of a zinc finger protein binding a sequence upstream of the A20 gene

<p>Abstract</p> <p>Background</p> <p>Artificial transcription factors (ATFs) are composed of DNA-binding and functional domains. These domains can be fused together to create proteins that can bind a chosen DNA sequence. To construct a valid ATF, it is necessary to design suitable DNA-binding and functional domains. The Cys₂-His₂zinc finger motif is the ideal structural scaffold on which to construct a sequence-specific protein. A20 is a cytoplasmic zinc finger protein that inhibits nuclear factor kappa-B activity and tumor necrosis factor (TNF)-mediated programmed cell death. A20 has been shown to prevent TNF-induced cytotoxicity in a variety of cell types including fibroblasts, B lymphocytes, WEHI 164 cells, NIH 3T3 cells and endothelial cells.</p> <p>Results</p> <p>In order to design a zinc finger protein (ZFP) structural domain that binds specific target sequences in the A20 gene promoter region, the structure and sequence composition of this promoter were analyzed by bioinformatics methods. The target sequences in the A20 promoter were submitted to the on-line ZF Tools server of the Barbas Laboratory, Scripps Research Institute (TSRI), to obtain a specific 18 bp target sequence and also the amino acid sequence of a ZFP that would bind to it. Sequence characterization and structural modeling of the predicted ZFP were performed by bioinformatics methods. The optimized DNA sequence of this artificial ZFP was recombined into the eukaryotic expression vector pIRES2-EGFP to construct pIRES2-EGFP/ZFP-flag recombinants, and the expression and biological activity of the ZFP were analyzed by RT-PCR, western blotting and EMSA, respectively. The ZFP was designed successfully and exhibited biological activity.</p> <p>Conclusion</p> <p>It is feasible to design specific zinc finger proteins by bioinformatics methods.</p

A Surface-Enhanced Raman Scattering Sensor Integrated with Battery-Controlled Fluidic Device for Capture and Detection of Trace Small Molecules

For surface-enhanced Raman scattering (SERS) sensors, one of the important issues is the development of substrates not only with high SERS-activity but also with strong ability to capture analytes. However, it is difficult to achieve the two goals simultaneously especially when detecting small molecules. Herein a compact battery-controlled nanostructure-assembled SERS system has been demonstrated for capture and detection of trace small molecule pollutants in water. In this SERS fluidic system, an electrical heating constantan wire covered with the vertically aligned ZnO nanotapers decorated with Ag-nanoparticles is inserted into a glass capillary. A mixture of thermo-responsive microgels, Au-nanorods colloids and analyte solution is then filled into the remnant space of the capillary. When the system is heated by switching on the battery, the thermo-responsive microgels shrink, which immobilizes the analyte and drives the Au-nanorod close to each other and close to the Ag-ZnO nanotapers. This process has also created high-density “hot spots” due to multi-type plasmonic couplings in three-dimensional space, amplifying the SERS signal. This integrated device has been successfully used to measure methyl parathion in lake water, showing a great potential in detection of aquatic pollutants

Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut

Objective: Gut microbiota is a newly identified risk factor for stroke, and there are no large prospective studies linking the baseline gut microbiome to long-term risk of stroke. We present here the correlation between the gut microbiota and stroke risk in people with no prior stroke history.Methods: A total of 141 participants aged ≥60 years without prior history of stroke were recruited and divided into low-risk, medium-risk, and high-risk groups based on known risk factors and whether they were suffering from chronic diseases. The composition of their gut microbiomes was compared using 16S rRNA gene amplicon next-generation-sequencing and Quantitative Insights into Microbial Ecology (QIIME) analysis. Levels of fecal short-chain fatty acids were measured using gas chromatography.Results: We found that opportunistic pathogens (e.g., Enterobacteriaceae and Veillonellaceae) and lactate-producing bacteria (e.g., Bifidobacterium and Lactobacillus) were enriched, while butyrate-producing bacteria (e.g., Lachnospiraceae and Ruminococcaceae) were depleted, in the high-risk group compared to the low-risk group. Butyrate concentrations were also lower in the fecal samples obtained from the high-risk group than from the low-risk group. The concentrations of other short-chain fatty acids (e.g., acetate, propionate, isobutyrate, isovalerate, and valerate) in the gut were comparable among the three groups.Conclusion: Participants at high risk of stroke were characterized by the enrichment of opportunistic pathogens, low abundance of butyrate-producing bacteria, and reduced concentrations of fecal butyrate. More researches into the gut microbiota as a risk factor in stroke should be carried out in the near future

Mapping topology-disorder phase diagram with a quantum simulator

We explore the topology-disorder phase diagram by simulating one-dimensional Su-Schrieffer-Heeger (SSH) model with quasiperiodic disorder using a programmable superconducting simulator. We experimentally map out and identify various trivial and topological phases with extended and localized bulk states. We find that in the topological phase the bulk states can be critically localized without mobility edge or contain both critically and completely localized states. In addition, there exist trivial and topological intermediate phases with mobility edge and coexistence of extended and completely localized states. The presence of the surprisingly rich phases in the simple SSH model with quasiperiodic disorder sheds new light on the investigation of the topological and localization phenomena in condensed-matter physics.Comment: 5 pages, 4 figure

Nanoporous Ag-Decorated Ag7O8NO3 Micro-Pyramids for Sensitive Surface-Enhanced Raman Scattering Detection

Porous noble metal nanomaterials can be employed to construct sensitive surface-enhanced Raman scattering (SERS) substrates, because the plasmonic nanopores and nanogaps of the porous materials can provide a larger number of hotspots, and can also serve as containers of analyte molecules. However, the fabrication processes of nanoporous noble metal are generally complicated. Here, a facile method is presented to prepare nanoporous Ag nanoparticles-decorated Ag7O8NO3 micro-pyramids, which are fabricated through the chemical reduction of the electrodeposited Ag7O8NO3 micro-pyramids using NaBH4. The Ag7O8NO3 micro-pyramids are fabricated by electrodeposition by using a simple aqueous solution of AgNO3 as electrolyte. Then, porous Ag-decorated Ag7O8NO3 micro-pyramids are achieved by the chemical reduction of the surface of the electrodeposited Ag7O8NO3 micro-pyramids with NaBH4. The high-density nanopores and nanogaps of the fabricated nanoporous Ag can provide plenty of hot spots for Raman enhancement. Additionally, the nanopores have an effective capacity to trap and enrich analytes. Using rhodamine 6G (R6G) as a probe molecule, the SERS performance of the fabricated SERS substrate has been investigated. It is found that a limit of detection (LOD) ~1.0 &times; 10&minus;15 M can be achieved for R6G. Then, the SERS substrates are employed to detect dye molecule (crystal violet) and pesticide (thiram), and their LODs are calculated down to 9.6 &times; 10&minus;13 M and 1.3 &times; 10&minus;15 M, respectively. The enhancement factor of the fabricated SERS substrate is estimated to be as high as 5.6 &times; 108. Therefore, the nanoporous Ag-decorated Ag7O8NO3 micro-pyramids have shown promising application in the sensitive SERS detection of organic molecules

Nanoporous Ag-Decorated Ag₇O₈NO₃ Micro-Pyramids for Sensitive Surface-Enhanced Raman Scattering Detection

Porous noble metal nanomaterials can be employed to construct sensitive surface-enhanced Raman scattering (SERS) substrates, because the plasmonic nanopores and nanogaps of the porous materials can provide a larger number of hotspots, and can also serve as containers of analyte molecules. However, the fabrication processes of nanoporous noble metal are generally complicated. Here, a facile method is presented to prepare nanoporous Ag nanoparticles-decorated Ag7O8NO3 micro-pyramids, which are fabricated through the chemical reduction of the electrodeposited Ag7O8NO3 micro-pyramids using NaBH4. The Ag7O8NO3 micro-pyramids are fabricated by electrodeposition by using a simple aqueous solution of AgNO3 as electrolyte. Then, porous Ag-decorated Ag7O8NO3 micro-pyramids are achieved by the chemical reduction of the surface of the electrodeposited Ag7O8NO3 micro-pyramids with NaBH4. The high-density nanopores and nanogaps of the fabricated nanoporous Ag can provide plenty of hot spots for Raman enhancement. Additionally, the nanopores have an effective capacity to trap and enrich analytes. Using rhodamine 6G (R6G) as a probe molecule, the SERS performance of the fabricated SERS substrate has been investigated. It is found that a limit of detection (LOD) ~1.0 × 10−15 M can be achieved for R6G. Then, the SERS substrates are employed to detect dye molecule (crystal violet) and pesticide (thiram), and their LODs are calculated down to 9.6 × 10−13 M and 1.3 × 10−15 M, respectively. The enhancement factor of the fabricated SERS substrate is estimated to be as high as 5.6 × 108. Therefore, the nanoporous Ag-decorated Ag7O8NO3 micro-pyramids have shown promising application in the sensitive SERS detection of organic molecules

Recyclable Multifunctional Magnetic Fe₃O₄@SiO₂@Au Core/Shell Nanoparticles for SERS Detection of Hg (II)

Mercury ions can be enriched along the food chain and even low concentrations of mercury ions can seriously affect human health and the environment. Therefore, rapid, sensitive, and highly selective detection of mercury ions is of great significance. In this work, we synthesized Fe3O4@SiO2@Au three-layer core/shell nanoparticles, and then modified 4-MPy (4-mercaptopyridine) to form a SERS sensor. Mercury ions in water can be easily captured by 4-MPy which were used as the reporter molecules, and the concentration of mercury ions can be evaluated based on the spectral changes (intensification and reduction of peaks) from 4-MPy. After the mercury ion was combined with the pyridine ring, the peak intensity at 1093 cm−1 increased with the concentration of mercury ion in the range of 10 ppm–1 ppb, while the Raman intensity ratio I (416 cm−1)/I (436 cm−1) decreased with the increase of mercury ion concentration. This magnetically separatable and recyclable SERS sensor demonstrates good stability, accuracy, and anti-interference ability and shows the potential to detect actual samples. Furthermore, we demonstrate that the probe is applicable for Hg2+ imaging in macrophage cells

Ordered arrays of Ag nanodendrite clusters as effective surface-enhanced Raman scattering substrates

We report a cheap synthetic approach to large-area ordered Ag nanodendrite cluster arrays as effective surface-enhanced Raman scattering (SERS) substrates, on a Zn plate coated with periodical porous photoresist via galvanic replacement reaction of Zn and AgNO3 in aqueous solution. Due to the geometrical confinement of the porous photoresist template coated on the Zn plate, the well-positioned Ag nanodendrite clusters are distributed on the Zn plate in ordered arrays. It is demonstrated that citric acid is essential to the formation of the nanodendrite cluster arrays. The resultant Ag nanodendrite cluster arrays not only have high SERS-activity to rhodamine 6G with good signal reproducibility but also can identify thiram (a widely-used pesticide) even at 0.1 mu M level, showing potential in SERS-based detection of pesticide remnants in the environmentclose

Table1_Arrays of Ag-nanoparticles decorated TiO2 nanotubes as reusable three-dimensional surface-enhanced Raman scattering substrates for molecule detection.docx

Three-dimensional surface-enhanced Raman scattering (SERS) substrates usually provide more hot spots in the excitation light beam and higher sensitivity when compared with the two-dimensional counterpart. Here a simple approach is presented for the fabrication of arrays of Ag-nanoparticles decorated TiO2 nanotubes. Arrays of ZnO nanorods were fabricated in advance by a hydrothermal method. Then TiO2 nanotube arrays were achieved by immersing the arrays of ZnO nanorods in an aqueous solution of (NH4)2TiF6 for 1.5 h. Vertically aligned TiO2 nanotube arrays were modified with dense Ag nanoparticles by Ag mirror reaction. High density of Ag nanoparticles decorated on the fabricated TiO2 nanotubes provide plenty of hotspots for Raman enhancement. In addition, the fabricated array of Ag nanoparticles modified TiO2 nanotubes can serve as a reusable SERS substrate because of the photocatalytic activity of the TiO2 nanotubes. The SERS substrate adsorbed with analyte molecules can realize self-cleaning in deionized water after UV irradiation for 2.5 h. The sensitivity of the fabricated SERS substrate was investigated by the detection of organic dye molecules. The detectable concentration limits of rhodamine 6G (R6G), malachite green (MG) and methylene blue (MB) were found to be 10−12 M, 10−9 M and 10−8 M, respectively. The enhancement factor (EF) of the three-dimensional SERS substrate was estimated to be as high as ∼1.4×108. Therefore, the prepared Ag nanoparticles modified TiO2 nanotube arrays have promising potentials to be applied to rapid and trace SERS detection of organic chemicals.</p