Additional file 1 of Stachydrine ameliorates hypoxia reoxygenation injury of cardiomyocyte via enhancing SIRT1-Nrf2 pathway

Supplementary Material

Structure of an Extended HAUSP Fragment

<div><p>(A) Structure of a HAUSP fragment (residues 53–560) that contains both the substrate-binding (green) and the catalytic domains. Binding sites for ubiquitin and substrate are indicated. The linker sequences between these two domains have high-temperature factors and are flexible in the crystals.</p> <p>(B) A structure-based model showing HAUSP bound to an ubiquitylated MDM2. Only one ubiquitin moiety and the MDM2 peptide are shown in this model.</p></div

One-Step Synthesis of Water-Soluble MoS₂ Quantum Dots via a Hydrothermal Method as a Fluorescent Probe for Hyaluronidase Detection

In this work, a bottom-up strategy is developed to synthesize water-soluble molybdenum disulfide quantum dots (MoS₂ QDs) through a simple, one-step hydrothermal method using ammonium tetrathiomolybdate [(NH₄)₂MoS₄] as the precursor and hydrazine hydrate as the reducing agent. The as-synthesized MoS₂ QDs are few-layered with a narrow size distribution, and the average diameter is about 2.8 nm. The resultant QDs show excitation-dependent blue fluorescence due to the polydispersity of the QDs. Moreover, the fluorescence can be quenched by hyaluronic acid (HA)-functionalized gold nanoparticles through a photoinduced electron-transfer mechanism. Hyaluronidase (HAase), an endoglucosidase, can cleave HA into proangiogenic fragments and lead to the aggregation of gold nanoparticles. As a result, the electron transfer is blocked and fluorescence is recovered. On the basis of this principle, a novel fluorescence sensor for HAase is developed with a linear range from 1 to 50 U/mL and a detection limit of 0.7 U/mL

Structural Comparison of Peptide Binding by HAUSP Reveals a Consensus Sequence

<div><p>(A) MDM2 peptide (red) binds to the same surface groove as the p53 peptide (magenta). Residues from MDM2 and p53 are shown in yellow and green, respectively.</p> <p>(B) Superposition of three HAUSP-binding peptides derived from MDM2 (red), p53 (magenta), and EBNA1 (green). The HAUSP TRAF-like domain is shown in a transparent surface representation, with critical residues shown in brown.</p> <p>(C) Structural alignment of HAUSP-binding peptides reveals a consensus sequence. The HAUSP surface groove (in a transparent surface representation) for binding to the consensus tetrapeptide is shown in the left panel. The consensus sequence is shown in the right panel.</p></div

Structural Basis of MDM2 Recognition by HAUSP

<div><p>(A) Overall structure of the HAUSP TRAF-like domain bound to MDM2 peptide is shown in a ribbon diagram (left) and in a surface representation (right). The important MDM2 residues are highlighted in yellow.</p> <p>(B) A stereo view of the specific interactions between MDM2 and HAUSP. These interactions are more extensive than those between p53 and HAUSP. Hydrogen bonds are represented by red dashed lines. All interacting residues are labeled.</p></div

Structure of the HAUSP N-Terminal TRAF-Like Domain

<div><p>(A) Structure of the HAUSP TRAF-like domain in a ribbon diagram (left) and a surface representation (right). Secondary structural elements (left) and the putative substrate-binding groove (right) are labeled.</p> <p>(B) Sequence alignment of the HAUSP TRAF-like domain with other TRAF family members. Conserved residues are shown in yellow. Residues that interact with p53 through hydrogen bonds and van der Waals contacts are identified by green arrow heads and green squares, respectively. Residues that interact with MDM2 through hydrogen bonds and van der Waals contacts are indicated by red arrow heads and red squares, respectively. Conserved residues that are involved in binding to peptides in other TRAF family proteins, but not in HAUSP, are colored red and indicated by purple background.</p></div

Workflow, tools, and databases used to identify potential functional SNPs in CYP11B2.

<p>Workflow, tools, and databases used to identify potential functional SNPs in CYP11B2.</p

HAUSP Preferentially Forms a Stable HAUSP–MDM2 Complex in the Presence of Excess p53

<div><p>(A) The TRAF-like domain of HAUSP is responsible for binding to MDM2. Various HAUSP fragments were individually incubated with MDM2 protein (residues 170–423) and their interactions were examined by gel filtration. The results are summarized here.</p> <p>(B) Identification of a minimal HAUSP-binding element in MDM2. Various MDM2 fragments were individually incubated with HAUSP TRAF-like domain (residues 53–206) and their interactions were examined by gel filtration. The results are summarized here.</p> <p>(C) HAUSP preferentially forms a stable HAUSP–MDM2 complex in the presence of excess p53. HAUSP (residues 1–206) interacts with both p53 (residues 351–382, upper panel) and MDM2 (residues 208–289, middle panel). However, in the presence of a 10-fold excess amount of p53, HAUSP formed a stable complex only with MDM2 (lower panel). The relevant peak fractions were visualized by SDS-PAGE followed by Coomassie staining.</p> <p>(D) Determination of binding affinities between the HAUSP TRAF-like domain (residues 53–206) and peptides derived from p53 and MDM2 by ITC. The p53 and MDM2 peptides contain residues 351–382 and 208–242, respectively. The binding affinities for the p53 and MDM2 peptides are 3 and 21 μM, respectively.</p></div

Association between IL-6-174G/C Polymorphism and the Risk of Sepsis and Mortality: A Systematic Review and Meta-Analysis

<div><p>Background</p><p>Recent studies have reported the association between IL-6-174G/C polymorphism and sepsis. However, the results are inconclusive and conflicting. To better understand the role of IL-6-174G/C polymorphism in sepsis, we conducted a comprehensive meta-analysis.</p><p>Methodology</p><p>Literature search was conducted through PubMed, Embase, Web of Knowledge databases until July 29, 2013. The pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using fixed- or random-effect model based on heterogeneity test in total and subgroup analyses.</p><p>Results</p><p>Twenty studies on the risk of sepsis and seven studies on sepsis mortality were included. None of the results showed evidence of a significant association between IL-6-174G/C polymorphism and sepsis risk in overall analysis or subgroup analyses based on sepsis type, ethnicity, source of control and age under any genetic model (the allele comparison, the codominant, the recessive or the dominant model). Although there was a statistically significant association between IL-6-174 G/C polymorphism and sepsis-related mortality under the recessive model, the significance did not exist after Bonferroni’s correction.</p><p>Conclusions</p><p>Current evidence does not support a direct effect of IL-6-174 G/C polymorphism on the risk of sepsis. In addition, there was no association between IL-6-174 G/C polymorphism and sepsis mortality after Bonferroni’s correction. Further analyses of gene-environment interactions and more studies based on larger sample size and homogeneous sepsis patients are required.</p></div

Additional file 6: of IMP1 regulates UCA1-mediated cell invasion through facilitating UCA1 decay and decreasing the sponge effect of UCA1 for miR-122-5p

Table S2. miRNAs associated with UCA1. (DOCX 13 kb