4D label-free proteomics analysis of oxygen-induced retinopathy with or without anti-VEGF treatment.

Oxygen-induced retinopathy (OIR) animal model is widely used for retinopathy of prematurity (ROP) researches. The purpose of this study was to identify proteins and related pathways of OIR with or without anti-vascular endothelial growth factor (VEGF) treatment, for use as biomarkers in diagnosing and treating ROP. Nine samples were subjected to proteomic analysis. Retina specimens were collected from 3 OIR mice, 3 OIR mice with anti-VEGF treatment and 3 normal mice (control group). Liquid chromatography-tandem mass spectrometry analysis was performed using the 4D label-free technique. Statistically significant differentially expressed proteins, gene ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway representations, InterPro (IPR) and protein interactions were analyzed. In total, 4585 unique proteins were identified as differentially expressed proteins (DEPs). Enrichment analysis of the GO and KEGG indicated functional clusters related to peptide biosynthetic and metabolic process, cellular macromolecule biosynthetic process and nucleic acid binding in OIR group. For anti-VEGF treatment group, DEPs were clustered in DNA replication, PI3K/Akt signaling pathway and Jak/STAT signaling pathway. Proteomic profiling is useful for the exploration of molecular mechanisms of OIR and mechanisms of anti-VEGF treatment. These findings may be useful for identification of novel biomarkers for ROP pathogenesis and treatment.

Prediction of protein-coding small ORFs in multi-species using integrated sequence-derived features and the random forest model.

Proteins encoded by small open reading frames (sORFs) can serve as functional elements playing important roles in vivo. Such sORFs also constitute the potential pool for facilitating the de novo gene birth, driving evolutionary innovation and species diversity. Therefore, their theoretical and experimental identification has become a critical issue. Herein, we proposed a protein-coding sORFs prediction method merely based on integrative sequence-derived features. Our prediction performance is better or comparable compared with other nine prevalent methods, which shows that our method can provide a relatively reliable research tool for the prediction of protein-coding sORFs. Our method allows users to estimate the potential expression of a queried sORF, which has been demonstrated by the correlation analysis between our possibility estimation and codon adaption index (CAI). Based on the features that we used, we demonstrated that the sequence features of the protein-coding sORFs in the two domains have significant differences implying that it might be a relatively hard task in terms of cross-domain prediction, hence domain-specific models were developed, which allowed users to predict protein-coding sORFs both in eukaryotes and prokaryotes. Finally, a web-server was developed and provided to boost and facilitate the study of the related field, which is freely available at http://guolab.whu.edu.cn/codingCapacity/index.html.

Unlocking a Dual-Channel Pathway in CO2 Hydrogenation to Methanol over Single-Site Zirconium on Amorphous Silica.

Converting CO2 into methanol on a large scale is of great significance in the sustainable methanol economy. Zirconia species are considered to be an essential support in Cu-based catalysts due to their excellent properties for CO2 adsorption and activation. However, the evolution of Zr species during the reaction and the effect of their structure on the reaction pathways remain unclear. Herein, single-site Zr species in an amorphous SiO2 matrix are created by enhancing the Zr-Si interaction in Cu/ZrO2 -SiO2 catalysts. In situ X-ray absorption spectroscopy (XAS) reveals that the coordination environment of single-site Zr is sensitive to the atmosphere and reaction conditions. We demonstrate that the CO2 adsorption occurs preferably on the interface of Cu and single-site Zr rather than on ZrO2 nanoparticles. Methanol synthesis in reverse water-gas-shift (RWGS)+CO-hydro pathway is verified only over single-dispersed Zr sites, whereas the ordinary formate pathway occurs on ZrO2 nanoparticles. Thus, it expands a non-competitive parallel pathway as a supplement to the dominant formate pathway, resulting in the enhancement of Cu activity sixfold and twofold based on Cu/SiO2 and Cu/ZrO2 catalysts, respectively. The establishment of this dual-channel pathway by single-site Zr species in this work opens new horizons for understanding the role of atomically dispersed oxides in catalysis science.

GBCdb: RNA expression landscapes and ncRNA-mRNA interactions in gallbladder carcinoma.

Gallbladder carcinoma (GBC), an aggressive malignant tumor of the biliary system, is characterized by high cellular heterogeneity and poor prognosis. Fewer data have been reported in GBC than other common cancer types. Multi-omics data will contribute to the understanding of the molecular mechanisms of cancer, cancer diagnosis and prognosis. Herein, to provide better understanding of the molecular events in GBC pathogenesis, we developed GBCdb ( http://tmliang.cn/gbc/ ), a user-friendly interface for the query and browsing of GBC-associated genes and RNA interaction networks using published multi-omics data, which also included experimentally supported data from different molecular levels. GBCdb will help to elucidate the potential biological roles of different RNAs and allow for the exploration of RNA interactions in GBC. These resources will provide an opportunity for unraveling the potential molecular features of Gallbladder carcinoma.

A comprehensive pan-cancer analysis reveals cancer-associated robust isomiR expression landscapes in miRNA arm switching.

MicroRNAs (miRNAs), important regulators of gene expression, play critical roles in various biological processes and tumorigenesis. To reveal the potential relationships between multiple isomiRs and arm switching, we performed a comprehensive pan-cancer analysis to discuss their roles in tumorigenesis and cancer prognosis. Our results showed that many miR-#-5p and miR-#-3p pairs from the two arms of pre-miRNA may have abundant expression levels, and they are often involved in distinct functional regulatory networks by targeting different mRNAs, although they may also interact with common targets. The two arms may show diverse isomiR expression landscapes, and their expression ratio might vary, mainly depending on tissue type. Dominantly expressed isomiRs can be used to determine distinct cancer subtypes that are associated with clinical outcome, indicating that they may be potential prognostic biomarkers. Our findings indicate robust and flexible isomiR expression landscapes that will enrich the study of miRNAs/isomiRs and aid in revealing the potential roles of multiple isomiRs yielded by arm switching in tumorigenesis.

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments.

Long non-coding RNAs (lncRNAs) play important functional roles in many diverse biological processes. However, not all expressed lncRNAs are functional. Thus, it is necessary to manually collect all experimentally validated functional lncRNAs (EVlncRNA) with their sequences, structures, and functions annotated in a central database. The first release of such a database (EVLncRNAs) was made using the literature prior to 1 May 2016. Since then (till 15 May 2020), 19 245 articles related to lncRNAs have been published. In EVLncRNAs 2.0, these articles were manually examined for a major expansion of the data collected. Specifically, the number of annotated EVlncRNAs, associated diseases, lncRNA-disease associations, and interaction records were increased by 260%, 320%, 484% and 537%, respectively. Moreover, the database has added several new categories: 8 lncRNA structures, 33 exosomal lncRNAs, 188 circular RNAs, and 1079 drug-resistant, chemoresistant, and stress-resistant lncRNAs. All records have checked against known retraction and fake articles. This release also comes with a highly interactive visual interaction network that facilitates users to track the underlying relations among lncRNAs, miRNAs, proteins, genes and other functional elements. Furthermore, it provides links to four new bioinformatics tools with improved data browsing and searching functionality. EVLncRNAs 2.0 is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs2/.

Probing the Nature of Zinc in Copper-Zinc-Zirconium Catalysts by Operando Spectroscopies for CO2 Hydrogenation to Methanol.

Active Zn species in Cu-based methanol synthesis catalysts have not been clearly identified yet due to their complex nature and dynamic structural changes during reactions. Herein, atomically dispersed Zn on ZrO2 support is established in Cu-based catalysts by separating Zn and Zr components from Cu (Cu-ZnZr) via the double-nozzle flame spray pyrolysis (DFSP) method. It exhibits superiority in methanol selectivity and yield compared to those with Cu-ZnO interface and isolated ZnO nanoparticles. Operando X-ray absorption spectroscopy (XAS) reveals that the atomically dispersed Zn species are induced during the reaction due to the strengthened Zn-Zr interaction. They can suppress formate decomposition to CO and decrease the H2 dissociation energy, shifting the reaction to methanol production. This work enlightens the rational design of unique Zn species by regulating coordination environments and offers a new perspective for exploring complex interactions in multi-component catalysts.

In Situ Investigations on Structural Evolutions during the Facile Synthesis of Cubic α-MoC1-x Catalysts.

Cubic α-phase molybdenum carbides (α-MoC1-x) exhibit great potential in hydrogen production at low temperatures due to their excellent activity in water dissociation. However, the design strategies of α-MoC1-x are severely restricted by the harsh synthesis conditions, which involve multistep ammonification and carburization or the utilization of a significant amount of noble metals. Herein, high-purity α-MoC1-x synthesis in a one-step carburization process was achieved with the assistance of a trace amount of Rh (0.02%). The structural evolution of Mo species during phase transition was monitored via qualitative and quantitative analysis by in situ X-ray diffraction (XRD) and in situ X-ray absorption spectroscopy (XAS), respectively. Environmental transmission electron microscopy (ETEM) was used to follow the visual changes. We reveal that the reduction of monoclinic MoO3 to cubic oxygen-deficient Mo oxide (MoOx) at low temperatures owing to the promoted H2 activation on Rh sites is vital to the following carbon atom insertion and transformation to α-MoC1-x, making the carburization follow the topological route. The systematic analysis of the relationship between the reduction behavior and the structural evolution supplies a feasible strategy for the α-MoC1-x synthesis, and in situ characterizations shed light on controlling the phase transformation during carburization.

Identification of Diagnostic Magnetic Resonance Imaging Findings in 47 Shoulders with Subcoracoid Impingement Syndrome by Comparison with 100 Normal Shoulders.

BACKGROUND The aim of this study was to identify the diagnostic magnetic resonance imaging (MRI) findings in 47 shoulders with subcoracoid impingement syndrome by comparison with 100 normal shoulders. MATERIAL AND METHODS The subcoracoid impingement syndrome group consisted of 47 shoulders with subcoracoid impingement syndrome and the normal group consisted of 100 normal shoulders. The MRI parameters - coracoids-humeral distance (CHD), coracoid index (CI), height of the lesser tuberosity (HLT), coracoid obliquity (CO), coracoglenoid angle (CGA), coracohumeral angle (CHA), width of the subscapular tendon (WST), and contact distance between subscapular tendon and coracoid process (CD) - were compared between the subcoracoid impingement syndrome group and the normal group. The areas under the curves (AUCs) from the receiver operating characteristic (ROC) for single MRI parameters were recorded, in which the MRI parameters with AUC exceeding 0.70 were included in the analysis of combined parameters. Comparisons of ROC were made among single parameters and combined parameters. RESULTS For diagnosing subcoracoid impingement syndrome by using single MRI parameters (CHD, CI, HLT, CGA, CHA, WST, and CD), the AUCs were 0.963, 0.806, 0.745, 0.691, 0.613, 0.685, and 0.614, respectively, of which CHD had the largest AUC. CHD, CI, and HLT (AUC exceeding 0.70) were included in the study of the combined parameters. The AUC of combined CHD and HLT showed a significantly larger AUC than that of CHD (0.986 vs 0.963, P=0.036), and showed no significant difference compared with that of combined CHD, CI, and HLT (0.986 vs 0.987, P=0.882). CONCLUSIONS Measurement of the coracoid-humeral distance and height of the lesser tuberosity were key MRI diagnostic findings for subcoracoid impingement syndrome.

Proteomics reveal biomethane production process induced by carbon nanotube.

Biomethane produced by methanogenic archaea is a main greenhouse resource of terrestrial and marine ecosystems, which strongly affects the global environment change. Conductive materials, especially nano-scale, show considerable intervention on biomethane production potential, but the mechanism is still unclear. Herein, we precisely quantified the absolute abundance of Methanosarcina spp. proteins affected by carbon nanotubes (CNTs) using tandem mass tag (TMT) proteomics technology. Among the 927 detectable proteins, more than three hundred, 304, showed differential expression. Gene Set Enrichment Analysis on KEGG pathways and GO biological processes revealed a trend of decreased protein synthesis induced by CNTs, suggesting these conductive nanomaterials may replace part of the cell structure and function. Interestingly, increased acetoclastic methanogenesis actually came at the expense of reduced protein synthesis in related pathways. CNTs stimulated biomethane production from acetate by stimulating intracellular redox activity and the -COOH oxidation process. These findings enhanced the understanding of the biomethane production process affected by conductive materials.

The Reliability of MyotonPRO in Assessing Masseter Muscle Stiffness and the Effect of Muscle Contraction.

BACKGROUND Temporomandibular disorders (TMD) are accompanied by masticatory muscle-related pain, making it meaningful to assess the stiffness of the masticatory muscles. The present study investigated the intra- and inter-operator reliabilities of MyotonPRO for assessing the elasticity of masseter muscles, to determine minimal detectable changes, and to quantify changes in stiffness from conditions of relaxation to maximal contraction. MATERIAL AND METHODS Twenty healthy subjects (10 men and 10 women) were recruited. The stiffness of their masseter muscles was quantified with MyotonPRO in both relaxed and maximal contraction conditions. Two experienced operators (A and B) measured stiffness on the same day, and operator A repeated this procedure 5 days later. RESULTS Intra-rater reliability was good (ICC=0.78) and inter-operator reliability was excellent (ICC=0.95) for assessing masseter muscle stiffness with MyotonPRO. The mean stiffness of the masseter muscle on the dominant side was 369.5 N/m under relaxed conditions and 618.3 N/m at maximum bite force, an increase of 67.4%. Stiffness on the dominant and non-dominant sides did not differ significantly under both conditions (P>0.05). CONCLUSIONS MyotonPRO is a reliable method for quantifying the stiffness of the masseter muscle and monitoring its changes under different contraction conditions.

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments.

Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs. However, these databases are small in scale (with a few hundreds of lncRNAs only) and specific in their focuses (plants, diseases or interactions). Thus, it is highly desirable to have a comprehensive dataset for experimentally validated lncRNAs as a central repository for all of their structures, functions and phenotypes. Here, we established EVLncRNAs by curating lncRNAs validated by low-throughput experiments (up to 1 May 2016) and integrating specific databases (lncRNAdb, LncRANDisease, Lnc2Cancer and PLNIncRBase) with additional functional and disease-specific information not covered previously. The current version of EVLncRNAs contains 1543 lncRNAs from 77 species that is 2.9 times larger than the current largest database for experimentally validated lncRNAs. Seventy-four percent lncRNA entries are partially or completely new, comparing to all existing experimentally validated databases. The established database allows users to browse, search and download as well as to submit experimentally validated lncRNAs. The database is available at http://biophy.dzu.edu.cn/EVLncRNAs.

Electroacupuncture improves neurogenic bladder dysfunction through activation of NGF/TrkA signaling in a rat model.

OBJECTIVE: To observe the effect of electroacupuncture on the morphological change of the bladder tissue and the protein expression levels of NGF, TrkA, p-TrkA, AKT, and p-AKT in the bladder tissue of rats with neurogenic bladder after suprasacral spinal cord injury and to preliminarily explore its partial mechanism of action. METHODS: Eighty female Sprague-Dawley rats were randomly divided into blank group, model group, electroacupuncture group, model/siNGF group, and electroacupuncture/siNGF group according to random number table method with 16 rats in each group. Eighty Neurogenic bladder models after suprasacral spinal cord injury were established by adopting a modified spinal cord transection method. Electroacupuncture intervention was conducted on the 19th day after modeling. The bladder function was detected by bladder weight, urine output, serum BUN, and urine protein. After treatment for 7 consecutive days, the rats were killed and the bladder tissues were removed rapidly for microscopic observation of morphological change after hematoxylin and eosin stain and for determination of the protein expression levels of NGF, TrkA, p-TrkA, AKT, and p-AKT via Western blot analysis. The transcription of NGF was measured by reverse-transcription polymerase chain reaction. RESULTS: After treatment, compared with the blank group, the bladder weight of model and electroacupuncture groups were significantly increased (P < 0.05). Compared with the model group, the bladder weight of the electroacupuncture group was decreased (P > 0.05). Compared with the blank group, the urine output of the model group was increased ( P < 0.05). Compared with the blank group, the urine output of the electroacupuncture group was increased ( P > 0.05). Compared with the blank group, the serum BUN of the model group was increased ( P < 0.05). Compared with the blank group, the serum BUN of the electroacupuncture group was increased ( P > 0.05). Compared with the blank group, the urine protein of the model group was increased ( P < 0.05). Compared with the blank group, the urine protein of the electroacupuncture group was increased ( P > 0.05). The expression of NGF, p-TrkA, and p-AKT in the model and electroacupuncture groups was obviously higher than that in the blank group ( P < 0.05). The expression of NGF, p-TrkA, and p-AKT in the electroacupuncture group was higher than that in the model group. The expression of TrkA and AKT were unchanged in blank, model, and electroacupuncture groups ( P > 0.05). After tail vein injection with siNGF lentivirus, the expression of NGF in the model/siNGF group and electroacupuncture/siNGF group was significantly decreased ( P < 0.05). And the protein level of p-AKT and p-TrkA was significantly lower than that of the model and electroacupuncture groups ( P < 0.05). CONCLUSION: Sacral electroacupuncture therapy can improve the expression of both NGF/TrkA signaling and AKT signaling in the local nerve of the damaged spinal cord, inhibit apoptosis of the damaged spinal cord, protect nerve cells, and promote the recovery of the damaged nerve. At the same time, electroacupuncture can promote the coordination of micturition reflex and improve neurogenic bladder function after the spinal cord injury.

A novel numerical model for protein sequences analysis based on spherical coordinates and multiple physicochemical properties of amino acids.

How to characterize short protein sequences to make an effective connection to their functions is an unsolved problem. Here we propose to map the physicochemical properties of each amino acid onto unit spheres so that each protein sequence can be represented quantitatively. We demonstrate the usefulness of this representation by applying it to the prediction of cell penetrating peptides. We show that its combination with traditional composition features yields the best performance across different datasets, among several methods compared. For the convenience of users, a web server has been established for automatic calculations of the proposed features at http://biophy.dzu.edu.cn/SNumD/.

Fast-Folding Pathways of the Thrombin-Binding Aptamer G-Quadruplex Revealed by a Markov State Model.

G-quadruplex structures participate in many important cellular processes. For a better understanding of their functions, knowledge of the mechanism by which they fold into the functional native structures is necessary. In this work, we studied the folding process of the thrombin-binding aptamer G-quadruplex. Enabled by a computational paradigm that couples an advanced sampling method and a Markov state model, four folding intermediates were identified, including an antiparallel G-hairpin, two G-triplex structures, and a double-hairpin conformation. Likewise, a misfolded structure with a nonnative distribution of syn/anti guanines was also observed. Based on these states, a transition path analysis revealed three fast-folding pathways, along which the thrombin-binding aptamer would fold to the native state directly, with no evidence of potential nonnative competing conformations. The results also showed that the TGT-loop plays an important role in the folding process. The findings of this research may provide general insight about the folding of other G-quadruplex structures.

Exploration of the folding dynamics of human telomeric G-quadruplex with a hybrid atomistic structure-based model.

Structure-based models or Go-like models, which are built from one or multiple particular experimental structures, have been successfully applied to the folding of proteins and RNAs. Recently, a variant termed the hybrid atomistic model advances the description of backbone and side chain interactions of traditional structure-based models, by borrowing the description of local interactions from classical force fields. In this study, we assessed the validity of this model in the folding problem of human telomeric DNA G-quadruplex, where local dihedral terms play important roles. A two-state model was developed and a set of molecular dynamics simulations was conducted to study the folding dynamics of sequence Htel24, which was experimentally validated to adopt two different (3 + 1) hybrid G-quadruplex topologies in K+ solution. Consistent with the experimental observations, the hybrid-1 conformation was found to be more stable and the hybrid-2 conformation was kinetically more favored. The simulations revealed that the hybrid-2 conformation folded in a higher cooperative manner, which may be the reason why it was kinetically more accessible. Moreover, by building a Markov state model, a two-quartet G-quadruplex state and a misfolded state were identified as competing states to complicate the folding process of Htel24. Besides, the simulations also showed that the transition between hybrid-1 and hybrid-2 conformations may proceed an ensemble of hairpin structures. The hybrid atomistic structure-based model reproduced the kinetic partitioning folding dynamics of Htel24 between two different folds, and thus can be used to study the complex folding processes of other G-quadruplex structures.

DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins.

BACKGROUND: Intrinsically unstructured or disordered proteins function via interacting with other molecules. Annotation of these binding sites is the first step for mapping functional impact of genetic variants in coding regions of human and other genomes, considering that a significant portion of eukaryotic genomes code for intrinsically disordered regions in proteins. RESULTS: DisBind (available at http://biophy.dzu.edu.cn/DisBind ) is a collection of experimentally supported binding sites in intrinsically disordered proteins and proteins with both structured and disordered regions. There are a total of 226 IDPs with functional site annotations. These IDPs contain 465 structured regions (ORs) and 428 IDRs according to annotation by DisProt. The database contains a total of 4232 binding residues (from UniProt and PDB structures) in which 2836 residues are in ORs and 1396 in IDRs. These binding sites are classified according to their interacting partners including proteins, RNA, DNA, metal ions and others with 2984, 258, 383, 350, and 262 annotated binding sites, respectively. Each entry contains site-specific annotations (structured regions, intrinsically disordered regions, and functional binding regions) that are experimentally supported according to PDB structures or annotations from UniProt. CONCLUSION: The searchable DisBind provides a reliable data resource for functional classification of intrinsically disordered proteins at the residue level.

Natural protein sequences are more intrinsically disordered than random sequences.

Most natural protein sequences have resulted from millions or even billions of years of evolution. How they differ from random sequences is not fully understood. Previous computational and experimental studies of random proteins generated from noncoding regions yielded inclusive results due to species-dependent codon biases and GC contents. Here, we approach this problem by investigating 10,000 sequences randomized at the amino acid level. Using well-established predictors for protein intrinsic disorder, we found that natural sequences have more long disordered regions than random sequences, even when random and natural sequences have the same overall composition of amino acid residues. We also showed that random sequences are as structured as natural sequences according to contents and length distributions of predicted secondary structure, although the structures from random sequences may be in a molten globular-like state, according to molecular dynamics simulations. The bias of natural sequences toward more intrinsic disorder suggests that natural sequences are created and evolved to avoid protein aggregation and increase functional diversity.

Analysis of the multi-copied genes and the impact of the redundant protein coding sequences on gene annotation in prokaryotic genomes.

The important roles of duplicated genes in evolutional process have been recognized in bacteria, archaebacteria and eukaryotes, while there is very little study on the multi-copied protein coding genes that share sequence identity of 100%. In this paper, the multi-copied protein coding genes in a number of prokaryotic genomes are comprehensively analyzed firstly. The results show that 0-15.93% of the protein coding genes in each genome are multi-copied genes and 0-16.49% of the protein coding genes in each genome are highly similar with the sequence identity ≥ 80%. Function and COG (Clusters of Orthologous Groups of proteins) analysis shows that 64.64% of multi-copied genes concentrate on the function of transposase and 86.28% of the COG assigned multi-copied genes concentrate on the COG code of 'L'. Furthermore, the impact of redundant protein coding sequences on the gene prediction results is studied. The results show that the problem of protein coding sequence redundancies cannot be ignored and the consistency of the gene annotation results before and after excluding the redundant sequences is negatively related with the sequences redundancy degree of the protein coding sequences in the training set.

A Novel Cylindrical Representation for Characterizing Intrinsic Properties of Protein Sequences.

The composition and sequence order of amino acid residues are the two most important characteristics to describe a protein sequence. Graphical representations facilitate visualization of biological sequences and produce biologically useful numerical descriptors. In this paper, we propose a novel cylindrical representation by placing the 20 amino acid residue types in a circle and sequence positions along the z axis. This representation allows visualization of the composition and sequence order of amino acids at the same time. Ten numerical descriptors and one weighted numerical descriptor have been developed to quantitatively describe intrinsic properties of protein sequences on the basis of the cylindrical model. Their applications to similarity/dissimilarity analysis of nine ND5 proteins indicated that these numerical descriptors are more effective than several classical numerical matrices. Thus, the cylindrical representation obtained here provides a new useful tool for visualizing and charactering protein sequences. An online server is available at http://biophy.dzu.edu.cn:8080/CNumD/input.jsp .