Manipulation of Multimodal and Multicolor Luminescence via Interplay of Traps and Rare Earth Emission Centers in Calcium Tungstate.

Multimodal luminescence involves color-tunable and wavelength manageable photon emissions upon variable luminescence pathways in response to different external stimuli, which provides clear visualization and high-level confidentiality for information encryption technologies. Integrating multimodal luminescence into a single matrix is regarded as a feasible strategy but remains a big challenge. In this work, multimodal (photoluminescence, persistent luminescence, upconversion luminescence, and thermally stimulated luminescence) and multicolor luminescence (green, yellow, orange, pink to red) is achieved in CaWO4:Yb3+,Er3+,Eu3+ phosphor by employing an interplay of traps and rare earth emission centers. Bright emission in a wide color gamut is achieved dynamically in response to thermal disturbance and light illumination, which further allows for on-demand emission manipulation in space and time dimensions. The compatible coexistence of multiple rare earth emissive centers together with abundant photoactive traps contributes to the excellent integration of multimodal photon emissions in calcium tungstate. This work provides a good example of integrating multimodal luminescence into one single matrix and indicates potential in advanced high-level information encryption applications.

Visualizing temperature inhomogeneity using thermo-responsive smart materials.

Despite the substantial progress made, the responsiveness of thermo-responsive materials upon various thermal fields is still restricted to monochromatic visualization with single-wavelength light emission. This stems from a poor understanding of the photophysical processes within the materials and the unvarying optical performance of luminescent centers' response to various ambient temperatures. Conventional techniques to assess the inhomogeneities of thermal fields can be time-consuming, require specialized equipment and suffer from inaccuracy due to the inevitable interference from background signals, especially at high temperature. To this end, we overcome these limitations for the first time, to flexibly visualize temperature inhomogeneities by developing a thermochromic smart material, SrGa12-xAlxO19:Dy3+. Two distinct modes of thermochromic properties (steady-state temperature-dependent luminescence and thermally stimulated luminescence) are investigated. It is revealed that the abundant colors (from yellow, green to red) and amazing color-changing features are due to the superior optical integration of the host (SrGa12-xAlxO19) and dopant (Dy3+) emissions under specific thermal stimulations. We suggest that this thermo-responsive smart material can be used to realize highly efficient and simple visualization of invisible thermal distribution in industry and beyond.

iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals.

Mammals have evolved mechanisms to sense hypoxia and induce hypoxic responses. Recently, high-throughput techniques have greatly promoted global studies of protein expression changes during hypoxia and the identification of candidate genes associated with hypoxia-adaptive evolution, which have contributed to the understanding of the complex regulatory networks of hypoxia. In this study, we developed an integrated resource for the expression dynamics of proteins in response to hypoxia (iHypoxia), and this database contains 2589 expression events of 1944 proteins identified by low-throughput experiments (LTEs) and 422,553 quantitative expression events of 33,559 proteins identified by high-throughput experiments from five mammals that exhibit a response to hypoxia. Various experimental details, such as the hypoxic experimental conditions, expression patterns, and sample types, were carefully collected and integrated. Furthermore, 8788 candidate genes from diverse species inhabiting low-oxygen environments were also integrated. In addition, we conducted an orthologous search and computationally identified 394,141 proteins that may respond to hypoxia among 48 animals. An enrichment analysis of human proteins identified from LTEs shows that these proteins are enriched in certain drug targets and cancer genes. Annotation of known posttranslational modification (PTM) sites in the proteins identified by LTEs reveals that these proteins undergo extensive PTMs, particularly phosphorylation, ubiquitination, and acetylation. iHypoxia provides a convenient and user-friendly method for users to obtain hypoxia-related information of interest. We anticipate that iHypoxia, which is freely accessible at https://ihypoxia.omicsbio.info, will advance the understanding of hypoxia and serve as a valuable data resource.

qPTMplants: an integrative database of quantitative post-translational modifications in plants.

As a crucial molecular mechanism, post-translational modifications (PTMs) play critical roles in a wide range of biological processes in plants. Recent advances in mass spectrometry-based proteomic technologies have greatly accelerated the profiling and quantification of plant PTM events. Although several databases have been constructed to store plant PTM data, a resource including more plant species and more PTM types with quantitative dynamics still remains to be developed. In this paper, we present an integrative database of quantitative PTMs in plants named qPTMplants (http://qptmplants.omicsbio.info), which hosts 1 242 365 experimentally identified PTM events for 429 821 nonredundant sites on 123 551 proteins under 583 conditions for 23 PTM types in 43 plant species from 293 published studies, with 620 509 quantification events for 136 700 PTM sites on 55 361 proteins under 354 conditions. Moreover, the experimental details, such as conditions, samples, instruments and methods, were manually curated, while a variety of annotations, including the sequence and structural characteristics, were integrated into qPTMplants. Then, various search and browse functions were implemented to access the qPTMplants data in a user-friendly manner. Overall, we anticipate that the qPTMplants database will be a valuable resource for further research on PTMs in plants.

pCysMod: Prediction of Multiple Cysteine Modifications Based on Deep Learning Framework.

Thiol groups on cysteines can undergo multiple post-translational modifications (PTMs), acting as a molecular switch to maintain redox homeostasis and regulating a series of cell signaling transductions. Identification of sophistical protein cysteine modifications is crucial for dissecting its underlying regulatory mechanism. Instead of a time-consuming and labor-intensive experimental method, various computational methods have attracted intense research interest due to their convenience and low cost. Here, we developed the first comprehensive deep learning based tool pCysMod for multiple protein cysteine modification prediction, including S-nitrosylation, S-palmitoylation, S-sulfenylation, S-sulfhydration, and S-sulfinylation. Experimentally verified cysteine sites curated from literature and sites collected by other databases and predicting tools were integrated as benchmark dataset. Several protein sequence features were extracted and united into a deep learning model, and the hyperparameters were optimized by particle swarm optimization algorithms. Cross-validations indicated our model showed excellent robustness and outperformed existing tools, which was able to achieve an average AUC of 0.793, 0.807, 0.796, 0.793, and 0.876 for S-nitrosylation, S-palmitoylation, S-sulfenylation, S-sulfhydration, and S-sulfinylation, demonstrating pCysMod was stable and suitable for protein cysteine modification prediction. Besides, we constructed a comprehensive protein cysteine modification prediction web server based on this model to benefit the researches finding the potential modification sites of their interested proteins, which could be accessed at http://pcysmod.omicsbio.info. This work will undoubtedly greatly promote the study of protein cysteine modification and contribute to clarifying the biological regulation mechanisms of cysteine modification within and among the cells.

iCysMod: an integrative database for protein cysteine modifications in eukaryotes.

As important post-translational modifications, protein cysteine modifications (PCMs) occurring at cysteine thiol group play critical roles in the regulation of various biological processes in eukaryotes. Due to the rapid advancement of high-throughput proteomics technologies, a large number of PCM events have been identified but remain to be curated. Thus, an integrated resource of eukaryotic PCMs will be useful for the research community. In this work, we developed an integrative database for protein cysteine modifications in eukaryotes (iCysMod), which curated and hosted 108 030 PCM events for 85 747 experimentally identified sites on 31 483 proteins from 48 eukaryotes for 8 types of PCMs, including oxidation, S-nitrosylation (-SNO), S-glutathionylation (-SSG), disulfide formation (-SSR), S-sulfhydration (-SSH), S-sulfenylation (-SOH), S-sulfinylation (-SO2H) and S-palmitoylation (-S-palm). Then, browse and search options were provided for accessing the dataset, while various detailed information about the PCM events was well organized for visualization. With human dataset in iCysMod, the sequence features around the cysteine modification sites for each PCM type were analyzed, and the results indicated that various types of PCMs presented distinct sequence recognition preferences. Moreover, different PCMs can crosstalk with each other to synergistically orchestrate specific biological processes, and 37 841 PCM events involved in 119 types of PCM co-occurrences at the same cysteine residues were finally obtained. Taken together, we anticipate that the database of iCysMod would provide a useful resource for eukaryotic PCMs to facilitate related researches, while the online service is freely available at http://icysmod.omicsbio.info.