Visualization 2.mp4

3D rendering of 64× expanded B16-F10 cell

Visualization 1.mp4

3D rendering of unexpanded B16-F10 cells

Synthesis of a fumed silica-supported poly-3-(2-aminoethylamino)propylsiloxane platinum complex and its catalytic behavior in the hydrosilylation of olefins with triethoxysilane

<p>A novel fumed silica-supported bidentate nitrogen platinum complex was conveniently prepared from N-(2-aminoethyl)-3-aminopropyltriethoxysilane via immobilization on fumed silica followed by a reaction with hexachloroplatinic acid. The title complex was systematically characterized and analyzed by Fourier Transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and specific surface area analysis (BET). The resulting title complex was found to be efficient and stable in catalyzing the hydrosilylation reaction of olefins with triethoxysilane. Furthermore, the polymeric platinum complex could be separated by simple filtration and reused four times without any appreciable loss of catalytic activity.</p

Co-occurring protein phosphorylation are functionally associated

<div><p>Post-translational modifications (PTMs) add a further layer of complexity to the proteome and regulate a wide range of cellular protein functions. With the increasing number of known PTM sites, it becomes imperative to understand their functional interplays. In this study, we proposed a novel analytical strategy to explore functional relationships between PTM sites by testing their tendency to be modified together (co-occurrence) under the same condition, and applied it to proteome-wide human phosphorylation data collected under 88 different laboratory or physiological conditions. Co-occurring phosphorylation occurs significantly more frequently than randomly expected and include many known examples of cross-talk or functional connections. Such pairs, either within the same phosphoprotein or between interacting partners, are more likely to be in sequence or structural proximity, be phosphorylated by the same kinases, participate in similar biological processes, and show residue co-evolution across vertebrates. In addition, we also found that their co-occurrence states tend to be conserved in orthologous phosphosites in the mouse proteome. Together, our results support that the co-occurring phosphorylation are functionally associated. Comparison with existing methods further suggests that co-occurrence analysis can be a useful complement to uncover novel functional associations between PTM sites.</p></div

Characterization of co-occurring phosphorylation pairs between interacting proteins in the CCSB PPI set.

<p>(A) Co-occurring pairs located in phosphorylation enriched protein complexes [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005502#pcbi.1005502.ref015" target="_blank">15</a>] are enriched with small FET p-values. Compared with control pairs, co-occurring pairs are more likely to co-localize in the PPI interfaces (B), and be catalyzed by the same predicted kinases (C). (D) The mouse orthologous phosphosites of human co-occurring pairs also show the tendency of being modified under same conditions.</p

Co-occurrence of phosphorylation status can reflect known functional associations.

<p>(A) An example co-occurrence analysis on transcription factor c-Jun. There are four phosphosites (S58, T239, S243 and S249) on c-Jun. Their phosphorylation status (red: on, green: off) across 88 conditions are shown. For each pairwise combination of phosphosites, their joint phosphorylation status is summarized into a contingency table with four entries <i>n</i>_<i>ij</i> (<i>i,j</i> ∈ {0,1}), where <i>n</i>_<i>ij</i> denotes the number of times the site 1 is in state <i>i</i> site 2 is in state <i>j</i>. One-sided FET is used to test if two sites are phosphorylated together more often than expected. Consistent with the previous study that three sites (T239, S243 and S249) tend to be phosphorylated together to inhibit c-Jun’s activity in epithelial resting cells, their pairwise FET p-values are lower than their combination with S58. The most significant co-occurring pair is highlighted. (B) Cumulative distribution of co-occurrence FET p-values for 22 known cross-talk examples (red) are superimposed onto the p-values of all within-protein phosphosite pairs (blue). (C) Comparing the distribution co-occurrence FET p-values between 380 homo-functional pairs and 35 hetero-functional pairs.</p

Comparison between known cross-talk/homo-functional pairs (positive set) and hetero-functional pairs (negative set) across different p-value threshold.

<p>Comparison between known cross-talk/homo-functional pairs (positive set) and hetero-functional pairs (negative set) across different p-value threshold.</p

Comparison between the positive and negative sets between interacting proteins across different p-value thresholds.

<p>The positive set is defined as phosphosite pairs in which both sites are located within phosphorylation enriched protein complexes [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005502#pcbi.1005502.ref015" target="_blank">15</a>]. The negative set is defined as phosphosite pairs in which at least one site cannot be mapped to those complexes.</p

Cell growth rate.

<p>Cell growth in each group was detected using the MTT assay. Compared with the NC group (controls transfected by 1 irrelevant interference sequence), the growth rate of ICBD-1 cells was significantly decreased after Gab1 siRNA interference or VEGFR-2 siRNA interference, **<i>P</i><0.01. Compared with the un-transfected group, there was no significant change in the growth rate of ICBD-1 cells within the NC group.</p

DataSheet2_Comprehensive analysis of prognosis of cuproptosis-related oxidative stress genes in multiple myeloma.ZIP

Introduction: Multiple myeloma (MM) is a highly heterogeneous hematologic malignancy. The patients’ survival outcomes vary widely. Establishing a more accurate prognostic model is necessary to improve prognostic precision and guide clinical therapy.Methods: We developed an eight-gene model to assess the prognostic outcome of MM patients. Univariate Cox analysis, Least absolute shrinkage and selection operator (LASSO) regression, and multivariate Cox regression analyses were used to identify the significant genes and construct the model. Other independent databases were used to validate the model.Results: The results showed that the overall survival of patients in the high-risk group was signifificantly shorter compared with that of those in the low-risk group. The eight-gene model demonstrated high accuracy and reliability in predicting the prognosis of MM patients.Discussion: Our study provides a novel prognostic model for MM patients based on cuproptosis and oxidative stress. The eight-gene model can provide valid predictions for prognosis and guide personalized clinical treatment. Further studies are needed to validate the clinical utility of the model and explore potential therapeutic targets.</p