Neutron-gamma discrimination with broaden the lower limit of energy threshold using BP neural network

Neutron-gamma discrimination is a tough and significative in experimental neutrons measurements procedure, especially for low-energy neutrons signal discrimination. In this work, based on the Pulse Shape Discrimination (PSD) and Back-Propagation (BP) artificial neural networks, a neutron-gamma discrimination method is developed to broaden the lower limit of energy threshold with the hidden layer of 20 neurons. Compared with neutron-gamma discrimination method based on PSD only, the developed neutron-gamma discrimination method based on the PSD and BP-ANN can discriminate neutron and gamma-ray signals with low energy threshold, which can discriminate signals up to 99.93%. Moreover, this work can reduce the energy threshold from 350 keV to 70 keV, as well as the acquired data utilization increased from 60% to more than 99.9%, which overcome the hardware limitations and distinguish neutron and gamma-ray signals, effectively. The developed neutron-gamma discrimination method and the trained neural network can be directly used to other experimental neutrons measurements.

Changes of wound area and inflammatory factors in diabetic foot patients after comprehensive nursing of traditional Chinese medicine

OBJECTIVE

The aim of this study is to analyze the application effect of traditional Chinese medicine (TCM) comprehensive nursing in diabetic foot patients.

PATIENTS AND METHODS

230 patients with diabetic foot admitted to Third people's Hospital of Haikou from January 2019 to April 2022 were classified as two groups, which consisted of a control group (n = 95) and an experimental group (n = 135). The control group took routine nursing intervention, while the experimental group took TCM comprehensive nursing intervention. The effect of intervention was compared by inflammatory factors (B-FGF, EGF, VEGF, and PDGF), wound area, self-rated anxiety scale (SAS), and self-rated depression scale (SDS).

RESULTS

After nursing, the levels of B-FGF, EGF, VEGF, and PDGF were higher in the experimental group (all p < 0.05). The total effective rate of diabetic foot recovery in the experimental group was 94.87% (74/78), higher than 87.67% (64/73) in the control group (p = 0.026). After nursing, the scores of SAS and SDS in the experimental group were lower than those in the control group (all p < 0.05).

CONCLUSIONS

The application of TCM comprehensive nursing in diabetic foot patients can greatly change the levels of B-FGF, EGF, VEGF, and PDGF in wound tissue, promote the healing of ulcer surface, improve patients' anxiety and depression, and enhance the quality of life of patients.

LncRNA SNHG15 promotes the proliferation of nasopharyngeal carcinoma via sponging miR-141-3p to upregulate KLF9

OBJECTIVE

Long non-coding RNAs (lncRNAs) have been identified to exert an oncogenic or anti-tumor function in malignant tumors. LncRNA SNHG15 is verified to be an oncogene in hepatocellular carcinoma, colorectal cancer, and prostate cancer. In this paper, we mainly investigate the potential influence of SNHG15 on the progression of nasopharyngeal carcinoma (NPC).

PATIENTS AND METHODS

SNHG15 levels in NPC tissues and cell lines were detected by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). Correlation between SNHG15 level and prognosis of NPC patients was evaluated by the Kaplan-Meier method. Regulatory effects of SNHG15 on proliferative, colony formation abilities, and apoptosis of SUNE1 and CNE1 cells were assessed through a series of functional experiments. Potential miRNAs binding SNHG15 and the downstream gene of the microRNA (miRNA) were predicted by bioinformatics method, which was confirmed by Dual-Luciferase reporter gene assay and Western blot.

RESULTS

SNHG15 was upregulated in NPC tissues and cells. High level of SNHG15 indicated worse survival in NPC patients. Knockdown of SNHG15 markedly suppressed proliferative ability and induced apoptosis in SUNE1 and CNE1 cells. It is verified that miR-141-3p was the direct target binding SNHG15, and KLF9 was the downstream gene of miR-141-3p. SNHG15 was demonstrated to be a ceRNA to upregulate KLF9 by competitively binding miR-141-3p.

CONCLUSIONS

SNHG15 is upregulated in NPC tissues, and this aggravates the progression of NPC by absorbing miR-141-3p to upregulate KLF9.

DNA-templated silver nanoclusters: structural correlation and fluorescence modulation

12 years after the introduction of DNA-templated silver nanoclusters (DNA-AgNCs), exciting progress has been made and yet we are still in the midst of trying to fully understand this nanomaterial. The prominent excellence of DNA-AgNCs is undoubtedly its modulatable emission property, of which how variation in DNA templates causes emission tuning remains elusive. Based on the up-to-date DNA-AgNCs, we aim to establish the correlation between the structure/sequence of DNA templates and emission behaviour of AgNCs. Herein, we systematically present a wide-range of DNA-AgNCs based on the structural complexity of the DNA templates, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), triple-stranded DNA (tsDNA) and DNA nanostructures. For each DNA category, we discuss the emission property, quantum yield and synthesis condition of the respective AgNCs, before cross-comparing the impact of different DNA scaffolds on the properties of AgNCs. A future outlook for this area is given as a conclusion. By putting the information together, this review may shed new light on understanding DNA-AgNCs while we are expecting continuous breakthroughs in this field.

Tunneling-nanotube direction determination in neurons and astrocytes

A tunneling nanotube (TNT) is a newly discovered structure involved in cell-cell communication and is found in various types of cells. Here we identify S100A4 as an extracellular molecule and describe its role in attracting the growth direction of TNTs. Together with its putative receptor, receptor for advanced glycation end product, we demonstrate their involvement in TNT direction guidance. Our results further suggest a mechanism for direction guidance of TNTs. In TNT-initiating cells, p53 activates caspase-3, which leads to S100A4 cleavage and its subsequent decrease in cellular concentration. The decrease in cellular S100A4 induces the formation of a gradient of S100A4, from a low concentration in initiating cells toward a high concentration in target cells. This concentration gradient of S100A4 induces direction guidance for TNTs.

Structural genomics efforts at the Chinese Academy of Sciences and Peking University

Structural genomics efforts at the Chinese Academy of Sciences and Peking University are reported in this article. The major targets for the structural genomics project are targeted proteins expressed in human hematopoietic stem/progenitor cells, proteins related to blood diseases and other human proteins. Up to now 328 target genes have been constructed in expression vectors. Among them, more than 50% genes have been expressed in Escherichia coli, approximately 25% of the resulting proteins are soluble, and 35 proteins have been purified. Crystallization, data collection and structure determination are continuing. Experiences accumulated during this initial stage are useful for designing and applying high-throughput approaches in structural genomics.

Antibody/antigen affinity behavior in liquid environment with electrical impedance analysis of quartz crystal microbalances

Electrical impedance analysis has been used to study anti-human immunoglobulin G (anti-h IgG) adsorption and the subsequent human immunoglobulin G (hIgG) or rabbit immunoglobulin G (rIgG) affinity reaction in aqueous liquids on a polystyrene (PS)-modified quartz crystal microbalance (QCM) surface. Time-dependent adsorption data of both the frequency shift and the electrical equivalent parameters (motional resistance, shunt capacitance, quality factor, etc) are monitored. It was found that the motional resistance, R, increases while the resonance frequency, f, decreases during both the anti-h IgG immobilization and the subsequent affinity process. Decreasing f primarily arises from the increased mass loading. Increasing R indicates more power dissipation (increased losses) in the system. The change in motional resistance, delta R, in the affinity reaction is considerably larger than that in anti-h IgG immobilization adsorption process, although the resonant frequency shifts, delta f, are very close in these two processes. Specifically, for a saturated solution, the ratio of delta R/delta f is 9.45 x 10 (-3) Omega/Hz for anti-h IgG adsorption and 28.1 x 10 (-3) omega/Hz for anti-h IgG/hIgG binding respectively, indicating the increased power dissipation with the increasing binding molecules. The shunt capacitance changes little in the hIgG binding process ( approximately 0.01 pF).

Bacillus subtilis arsenate reductase is structurally and functionally similar to low molecular weight protein tyrosine phosphatases

Arsenate is an abundant oxyanion that, because of its ability to mimic the phosphate group, is toxic to cells. Arsenate reductase (EC; encoded by the arsC gene in bacteria) participates to achieve arsenate resistance in both prokaryotes and yeast by reducing arsenate to arsenite; the arsenite is then exported by a specific transporter. The crystal structure of Bacillus subtilis arsenate reductase in the reduced form with a bound sulfate ion in its active site is solved at 1.6-A resolution. Significant structural similarity is seen between arsenate reductase and bovine low molecular weight protein tyrosine phosphatase, despite very low sequence identity. The similarity is especially high between their active sites. It is further confirmed that this structural homology is relevant functionally by showing the phosphatase activity of the arsenate reductase in vitro. Thus, we can understand the arsenate reduction in the light of low molecular weight protein tyrosine phosphatase mechanism and also explain the catalytic roles of essential residues such as Cys-10, Cys-82, Cys-89, Arg-16, and Asp-105. A "triple cysteine redox relay" is proposed for the arsenate reduction mechanism.

Preparation and crystallization of a Bacillus subtilis arsenate reductase

Arsenate reductase (AR) in B. subtilis is encoded by the chromosomal arsC gene. Together with arsB and arsR, arsC participates in detoxification processes for the arsenate and arsenite ions. Full-length arsenate reductase without any modification has been expressed in Escherichia coli and purified in a soluble form. The recombinant protein has been crystallized at 277 K using polyethyleneglycol (PEG) or poly(ethyleneglycol) methyl ether (PME) as the main precipitant. At least two forms of crystals large enough for data collection have been obtained from wild-type protein under different conditions. An orthorhombic crystal diffracted to beyond 2.2 A with space group P2(1)2(1)2(1) and unit-cell parameters a = 51.22, b = 91.62, c = 101.93 A. A near-complete data set has been collected to 2.5 A. The application of the flash-annealing technique was crucial for high resolution during the data collection. The SeMet-substituted AR has also been produced and crystallized under very similar conditions as the wild type, but the unit-cell parameters are very different. The crystals of the SeMet protein diffracted to higher resolution than those of the wild type.

Insights into the functional architecture of the catalytic center of a maize beta-glucosidase Zm-p60.1

The maize (Zea mays) beta-glucosidase Zm-p60.1 has been implicated in regulation of plant development by the targeted release of free cytokinins from cytokinin-O-glucosides, their inactive storage forms. The crystal structure of the wild-type enzyme was solved at 2.05-A resolution, allowing molecular docking analysis to be conducted. This indicated that the enzyme specificity toward substrates with aryl aglycones is determined by aglycone aromatic system stacking with W373, and interactions with edges of F193, F200, and F461 located opposite W373 in a slot-like aglycone-binding site. These aglycone-active site interactions recently were hypothesized to determine substrate specificity in inactive enzyme substrate complexes of ZM-Glu1, an allozyme of Zm-p60.1. Here, we test this hypothesis by kinetic analysis of F193I/Y/W mutants. The decreased K(m) of all mutants confirmed the involvement of F193 in determining enzyme affinity toward substrates with an aromatic aglycone. It was unexpected that a 30-fold decrease in k(cat) was found in F193I mutant compared with the wild type. Kinetic analysis and computer modeling demonstrated that the F193-aglycone-W373 interaction not only contributes to aglycone recognition as hypothesized previously but also codetermines catalytic rate by fixing the glucosidic bond in an orientation favorable for attack by the catalytic pair, E186 and E401. The catalytic pair, assigned initially by their location in the structure, was confirmed by kinetic analysis of E186D/Q and E401D/Q mutants. It was unexpected that the E401D as well as C205S and C211S mutations dramatically impaired the assembly of a catalysis-competent homodimer, suggesting novel links between the active site structure and dimer formation.

Insights into the functional architecture of the catalytic center of a maize beta-glucosidase Zm-p60.1

The maize (Zea mays) beta-glucosidase Zm-p60.1 has been implicated in regulation of plant development by the targeted release of free cytokinins from cytokinin-O-glucosides, their inactive storage forms. The crystal structure of the wild-type enzyme was solved at 2.05-A resolution, allowing molecular docking analysis to be conducted. This indicated that the enzyme specificity toward substrates with aryl aglycones is determined by aglycone aromatic system stacking with W373, and interactions with edges of F193, F200, and F461 located opposite W373 in a slot-like aglycone-binding site. These aglycone-active site interactions recently were hypothesized to determine substrate specificity in inactive enzyme substrate complexes of ZM-Glu1, an allozyme of Zm-p60.1. Here, we test this hypothesis by kinetic analysis of F193I/Y/W mutants. The decreased K(m) of all mutants confirmed the involvement of F193 in determining enzyme affinity toward substrates with an aromatic aglycone. It was unexpected that a 30-fold decrease in k(cat) was found in F193I mutant compared with the wild type. Kinetic analysis and computer modeling demonstrated that the F193-aglycone-W373 interaction not only contributes to aglycone recognition as hypothesized previously but also codetermines catalytic rate by fixing the glucosidic bond in an orientation favorable for attack by the catalytic pair, E186 and E401. The catalytic pair, assigned initially by their location in the structure, was confirmed by kinetic analysis of E186D/Q and E401D/Q mutants. It was unexpected that the E401D as well as C205S and C211S mutations dramatically impaired the assembly of a catalysis-competent homodimer, suggesting novel links between the active site structure and dimer formation.

Purification, crystallization and preliminary X-ray analysis of a maize cytokinin glucoside specific beta-glucosidase

Zm-p60.1, a cytokinin glucoside specific beta-glucosidase from maize, is a key enzyme involved in plant development and growth. It has been overexpressed in soluble form from Escherichia coli with a His tag at its N-terminus. The recombinant protein has been purified and crystallized at room temperature using PEG 4000 as the main precipitant. At least three crystal forms have been observed from very similar growth conditions. A flash-annealed monoclinic crystal diffracted to high resolution (beyond 2 A) with space group P2(1) and unit-cell parameters a = 55.66, b = 110.72, c = 72.94 A, beta = 92.10 degrees. The asymmetric unit is estimated and confirmed by molecular-replacement solution to contain one Zm-p60.1 dimer, giving a crystal volume per protein mass (V(M)) of 1.89 A(3) Da(-1) and a solvent content of 35%.

Crystal structure of hemolin: a horseshoe shape with implications for homophilic adhesion

Hemolin, an insect immunoglobulin superfamily member, is a lipopolysaccharide-binding immune protein induced during bacterial infection. The 3.1 angstrom crystal structure reveals a bound phosphate and patches of positive charge, which may represent the lipopolysaccharide binding site, and a new and unexpected arrangement of four immunoglobulin-like domains forming a horseshoe. Sequence analysis and analytical ultracentrifugation suggest that the domain arrangement is a feature of the L1 family of neural cell adhesion molecules related to hemolin. These results are relevant to interpretation of human L1 mutations in neurological diseases and suggest a domain swapping model for how L1 family proteins mediate homophilic adhesion.

Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site

BACKGROUND

Ribonucleotide reductases (RNRs) catalyze the formation of the deoxyribonucleotides that are essential for DNA synthesis. The R2 subunit of Escherichia coli RNR is a homodimer containing one dinuclear iron centre per monomer. A tyrosyl radical is essential for catalysis, and is formed via a reaction in which the reduced, diferrous form of the iron centre activates dioxygen. To help understand the mechanism of oxygen activation, we examined the structure of the diferrous form of R2.

RESULTS

The crystal structures of reduced forms of both wild type R2 and a mutant of R2 (Ser211--> Ala) have been determined at 1.7 A and 2.2 A resolution, respectively. The diferrous iron centre was compared to the previously determined structure of the oxidized, diferric form of R2. In both forms of R2 the iron centre is coordinated by the same carboxylate dominated ligand sphere, but in the reduced form there are clear conformational changes in three of the carboxylate ligands and the bridging mu-oxo group and two water molecules are lost. In the reduced form of R2 the coordination number decreases from six to four for both ferrous ions, explaining their high reactivity towards dioxygen. The structure of the mutant Ser211--> Ala, known to have impaired reduction kinetics, shows a large conformational change in one of the neighbouring helices although the iron coordination is very similar to the wild type protein.

CONCLUSIONS

Carboxylate shifts are often important for carboxylate coordinated metal clusters; they allow the metals to achieve different coordination modes in redox reactions. In the case of reduced R2 these carboxylate shifts allow the formation of accessible reaction sites for dioxygen. The Ser211--> Ala mutant displays a conformational change in the helix containing the mutation, explaining its altered reduction kinetics.

The crystal structure of the iron-free cytochrome c peroxidase and its implication for the enzymatic mechanism

We report the refined structure of an iron-free form of cytochrome c peroxidase (CcP) at 2.3 A resolution. The backbone comparison between native CcP and iron-free CcP shows that the two structures have the same protein fold within experimental error. The only difference noted is in the heme pocket where the distance between the proximal histidine and the center of the protoporphyrin has increased. The results show that the iron-free CcP should be a good substitute for native CcP in fluorescence studies and thus also validate previous studies using iron-free CcPs as efficient fluorescent probes in electron transfer studies.

The crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase

Protein tyrosine phosphorylation and dephosphorylation are central reactions for control of cellular division, differentiation and development. Here we describe the crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase (PTPase), a cytosolic phosphatase present in many mammalian cells. The enzyme catalyses the dephosphorylation of phosphotyrosine-containing substrates, and overexpression of the protein in normal and transformed cells inhibits cell proliferation. The structure of the low-molecular-weight PTPase reveals an alpha/beta protein containing a phosphate-binding loop motif at the amino end of helix alpha 1. This motif includes the essential active-site residues Cys 12 and Arg 18 and bears striking similarities to the active-site motif recently described in the structure of human PTP1B. The structure of the low-molecular-weight PTPase supports a reaction mechanism involving the conserved Cys 12 as an attacking nucleophile in an in-line associative mechanism. The structure also suggests a catalytic role for Asp 129 in the reaction cycle.

Crystallisation of a low molecular weight phosphotyrosine protein phosphatase from bovine liver

Single crystals of a low molecular weight phosphotyrosine protein phosphatase from bovine liver have been grown. The crystals belong to space group P2(1)2(1)2(1), have cell dimensions a = 46.3 A, b = 62.2 A, c = 62.7 A and diffract to better than 2.0 A resolution. The crystals are well suited for high resolution X-ray studies.