DataSheet_1_Refractory Helicobacter pylori infection and the gastric microbiota.pdf

BackgroundCuring refractory Helicobacter pylori infection is difficult. In addition, there is currently no research on the gastric microbiota of refractory H. pylori infection.MethodsWe designed a clinical retrospective study involving 32 subjects divided into three groups: 1. nAGHp.a, treatment-naïve patients with H. pylori infection; 2. nAGHp.b, H. pylori-negative patients; and 3. EFHp.a, patients with refractory H. pylori infection. Gastric mucosal samples from the biobank of our research center were collected for 16S rRNA sequencing analysis and bacterial functions were predicted via PICRUSt.ResultsThere were significant differences between the H. pylori- positive group and the H. pylori-negative group in species diversity, gastric microbiota structure, and bacterial function. The beneficial Lactobacillus in the H. pylori-positive group were significantly enriched compared with those in the refractory H. pylori infection group. The bacterial interaction network diagram suggested that the microbiota interactions in the refractory H. pylori infection group decreased. The gastric microbiota of the refractory H. pylori infection group was enriched in the pathways of metabolism and infectious diseases (energy metabolism, bacterial secretion system, glutathione metabolism, protein folding and associated processing, sulphur metabolism, membrane and intracellular structural molecules, lipopolysaccharide biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, inorganic ion transport and metabolism, and metabolism of cofactors and vitamins) when compared with the H. pylori-positive group without treatment based on PICRUSt analysis.ConclusionSignificant alterations occurred in the gastric microbiota when eradication of H. pylori failed multiple times. A history of eradication of multiple H. pylori infections leads to an imbalance in the gastric mucosal microbiota to a certain extent, which was mainly reflected in the inhibition of the growth of beneficial Lactobacillus in the stomach. Patients with refractory H. pylori infection may be at a higher risk of developing gastric cancer than other H. pylori-positive patients.</p

Table_1_Refractory Helicobacter pylori infection and the gastric microbiota.docx

BackgroundCuring refractory Helicobacter pylori infection is difficult. In addition, there is currently no research on the gastric microbiota of refractory H. pylori infection.MethodsWe designed a clinical retrospective study involving 32 subjects divided into three groups: 1. nAGHp.a, treatment-naïve patients with H. pylori infection; 2. nAGHp.b, H. pylori-negative patients; and 3. EFHp.a, patients with refractory H. pylori infection. Gastric mucosal samples from the biobank of our research center were collected for 16S rRNA sequencing analysis and bacterial functions were predicted via PICRUSt.ResultsThere were significant differences between the H. pylori- positive group and the H. pylori-negative group in species diversity, gastric microbiota structure, and bacterial function. The beneficial Lactobacillus in the H. pylori-positive group were significantly enriched compared with those in the refractory H. pylori infection group. The bacterial interaction network diagram suggested that the microbiota interactions in the refractory H. pylori infection group decreased. The gastric microbiota of the refractory H. pylori infection group was enriched in the pathways of metabolism and infectious diseases (energy metabolism, bacterial secretion system, glutathione metabolism, protein folding and associated processing, sulphur metabolism, membrane and intracellular structural molecules, lipopolysaccharide biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, inorganic ion transport and metabolism, and metabolism of cofactors and vitamins) when compared with the H. pylori-positive group without treatment based on PICRUSt analysis.ConclusionSignificant alterations occurred in the gastric microbiota when eradication of H. pylori failed multiple times. A history of eradication of multiple H. pylori infections leads to an imbalance in the gastric mucosal microbiota to a certain extent, which was mainly reflected in the inhibition of the growth of beneficial Lactobacillus in the stomach. Patients with refractory H. pylori infection may be at a higher risk of developing gastric cancer than other H. pylori-positive patients.</p

Formation of an Interlocked Quadruplex Dimer by d(GGGT)

A tetranucleotide sequence d(GGGT) has been shown to self-assemble into an interlocking quadruplex dimer. UV-melting studies indicated the existence of two species that each showed distinct quadruplex melting transitions, a low-Tm species, Ql, and a high-Tm species, Qh. Conditions were controlled to favor the formation of either Ql or Qh. Ql and Qh each showed circular dichroism spectra characteristic of parallel quadruplexes. Negative ion nano-electrospray ionization mass spectrometry confirmed that Ql was a tetrameric complex, d(GGGT)4, and Qh was an octameric complex, d(GGGT)8. High-resolution 1H NMR spectroscopy evidenced that d(GGGT)4 was a C4-symmetric parallel tetramolecular quadruplex. The 1H NMR spectrum of d(GGGT)8 was consistent with a structure formed by the dimerization of a parallel, “slipped” tetramolecular quadruplex that has its diagonal strands staggered by one base. This “slippage” results in two guanine bases at the 5‘ end of the quadruplex being presented diagonally that are not involved in tetrads. Two such “slipped” quadruplexes dimerize via these free G-bases at the 5‘ ends by forming an extra G-tetrad. Each “slipped” quadruplex contributes two guanine bases to this extra G-tetrad. The formation of a novel GTGT tetrad is also observed at both the 3‘ ends of the interlocked quadruplex dimer

Image_1_Refractory Helicobacter pylori infection and the gastric microbiota.pdf

BackgroundCuring refractory Helicobacter pylori infection is difficult. In addition, there is currently no research on the gastric microbiota of refractory H. pylori infection.MethodsWe designed a clinical retrospective study involving 32 subjects divided into three groups: 1. nAGHp.a, treatment-naïve patients with H. pylori infection; 2. nAGHp.b, H. pylori-negative patients; and 3. EFHp.a, patients with refractory H. pylori infection. Gastric mucosal samples from the biobank of our research center were collected for 16S rRNA sequencing analysis and bacterial functions were predicted via PICRUSt.ResultsThere were significant differences between the H. pylori- positive group and the H. pylori-negative group in species diversity, gastric microbiota structure, and bacterial function. The beneficial Lactobacillus in the H. pylori-positive group were significantly enriched compared with those in the refractory H. pylori infection group. The bacterial interaction network diagram suggested that the microbiota interactions in the refractory H. pylori infection group decreased. The gastric microbiota of the refractory H. pylori infection group was enriched in the pathways of metabolism and infectious diseases (energy metabolism, bacterial secretion system, glutathione metabolism, protein folding and associated processing, sulphur metabolism, membrane and intracellular structural molecules, lipopolysaccharide biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, inorganic ion transport and metabolism, and metabolism of cofactors and vitamins) when compared with the H. pylori-positive group without treatment based on PICRUSt analysis.ConclusionSignificant alterations occurred in the gastric microbiota when eradication of H. pylori failed multiple times. A history of eradication of multiple H. pylori infections leads to an imbalance in the gastric mucosal microbiota to a certain extent, which was mainly reflected in the inhibition of the growth of beneficial Lactobacillus in the stomach. Patients with refractory H. pylori infection may be at a higher risk of developing gastric cancer than other H. pylori-positive patients.</p

Reversible Regulation of Protein Binding Affinity by a DNA Machine

We report a DNA machine that can reversibly regulate target binding affinity on the basis of distance-dependent bivalent binding. It is a tweezer-like DNA machine that can tune the spatial distance between two ligands to construct or destroy the bivalent binding. The DNA machine can strongly bind to the target protein when the ligands are placed at an appropriate distance but releases the target when the bivalent binding is disrupted by enlargement of the distance between the ligands. This “capture–release” cycle could be repeatedly driven by single-stranded DNA without changing the ligands and target protein

Domain-Confined Multiple Collision Enhanced Catalytic Soot Combustion over a Fe₂O₃/TiO₂–Nanotube Array Catalyst Prepared by Light-Assisted Cyclic Magnetic Adsorption

The ordered TiO₂ nanotube array (NA)-supported ferric oxide nanoparticles with adjustable content and controllable particulate size were prepared through a facile light-assisted cyclic magnetic adsorption (LCMA) method. Multiple techniques such as SEM, TEM, EDX, XRD, EXAFS, XPS, UV–vis absorption, and TG were employed to study the structure and properties of the catalysts. The influencing factors upon soot combustion including the annealing temperature and loading of the active component in Fe₂O₃/TiO₂–NA were also investigated. An obvious confinement effect on the catalytic combustion of soot was observed for the ferric oxide nanoparticles anchored inside TiO₂ nanotubes. On the basis of the catalytic performance and characterization results, a novel domain-confined multiple collision enhanced soot combustion mechanism was proposed to account for the observed confinement effect. The design strategy for such nanotube array catalysts with domain-confined macroporous structure is meaningful and could be well-referenced for the development of other advanced soot combustion catalysts

DNA-Grafted Polypeptide Molecular Bottlebrush Prepared via Ring-Opening Polymerization and Click Chemistry

A new type of DNA grafted polypeptide molecular brush was synthesized via a combination of ring-opening polymerization (ROP) and click chemistry. This conjugation method provides an easy and efficient approach to obtain a hybrid DNA-grafted polypeptide molecular bottlebrush. The structure and assembly behaviors of this hybrid brush were investigated using electrophoresis, UV–vis spectroscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM). Hierarchical supramolecular assemblies can be obtained through hybridization of two kinds of polypeptide-<i>g</i>-DNA molecular bottlebrushes containing complementary DNA side chains. We further demonstrated that such polypeptide-<i>g</i>-DNA can be hybridized with ds-DNA and DNA-grafted gold nanoparticles to form a supermolecular bottlebrush and hybrid bottlebrush, respectively. In addition, DNA-polypeptide hydrogel can be prepared by hybridization of polypeptide-<i>g</i>-DNA with a linker-ds-DNA, which contains the complementary “sticky ends” to serve as cross-linkers

In Situ Formation of Covalent Second Network in a DNA Supramolecular Hydrogel and Its Application for 3D Cell Imaging

DNA hydrogels have been demonstrated with important applications in three-dimensional cell culture in vitro due to their good biocompatibility, biodegradability, and permeability. In these applications, to observe the cell morphology and functions in situ, immobilization, labeling, and imaging processes are involved, which requires good stability of the hydrogels during washing and immersion. To improve the stability of the hydrogels for better imaging, here we built a covalent second network in a DNA supramolecular hydrogel by in situ polymerization and successfully constructed a stable three-dimensional transparent system for cell culture and observation. This strategy has been proved to be efficient in enhancing the mechanical properties and immobilizing the cells inside the hydrogel, which can be applied for immunostaining and cell imaging

An Electrochemically Actuated Reversible DNA Switch

In this Letter, we have realized the electrical actuation of a DNA molecular device in a rapid and reliable manner with a microfabricated chip. The three-electrode chip containing Ir, IrO2, and Ag electrodes deposited in designed shapes and positions on the SiO2 surface was made by photolithography and magnetron reaction sputter deposition technology. In this design, the negative feedback property enabled the system to rapidly change and maintain the solution pH at arbitrary value by water electrolysis. As a proof-of-concept, we can drive a DNA switch based on the opening and close of an i-motif structure by switching the potential between the working and reference electrodes between −304 and −149 mV. We have demonstrated that DNA can be electrically switched within seconds, without obvious decay of the fluorescence amplitudes for at least 30 cycles, suggesting that this DNA switch is rapid in response and fairly robust. We have also demonstrated that this device could manipulate the DNA switch automatically by using chronoamperometry

An Electrochemically Actuated Reversible DNA Switch

In this Letter, we have realized the electrical actuation of a DNA molecular device in a rapid and reliable manner with a microfabricated chip. The three-electrode chip containing Ir, IrO2, and Ag electrodes deposited in designed shapes and positions on the SiO2 surface was made by photolithography and magnetron reaction sputter deposition technology. In this design, the negative feedback property enabled the system to rapidly change and maintain the solution pH at arbitrary value by water electrolysis. As a proof-of-concept, we can drive a DNA switch based on the opening and close of an i-motif structure by switching the potential between the working and reference electrodes between −304 and −149 mV. We have demonstrated that DNA can be electrically switched within seconds, without obvious decay of the fluorescence amplitudes for at least 30 cycles, suggesting that this DNA switch is rapid in response and fairly robust. We have also demonstrated that this device could manipulate the DNA switch automatically by using chronoamperometry