Abstract
Motivation
Automated function prediction (AFP) of proteins is a large-scale multi-label classification problem. Two limitations of most network-based methods for AFP are (i) a single model ...must be trained for each species and (ii) protein sequence information is totally ignored. These limitations cause weaker performance than sequence-based methods. Thus, the challenge is how to develop a powerful network-based method for AFP to overcome these limitations.
Results
We propose DeepGraphGO, an end-to-end, multispecies graph neural network-based method for AFP, which makes the most of both protein sequence and high-order protein network information. Our multispecies strategy allows one single model to be trained for all species, indicating a larger number of training samples than existing methods. Extensive experiments with a large-scale dataset show that DeepGraphGO outperforms a number of competing state-of-the-art methods significantly, including DeepGOPlus and three representative network-based methods: GeneMANIA, deepNF and clusDCA. We further confirm the effectiveness of our multispecies strategy and the advantage of DeepGraphGO over so-called difficult proteins. Finally, we integrate DeepGraphGO into the state-of-the-art ensemble method, NetGO, as a component and achieve a further performance improvement.
Availability and implementation
https://github.com/yourh/DeepGraphGO.
Supplementary information
Supplementary data are available at Bioinformatics online.
Phase transformation is essentially important for the microstructures and properties of sol–gel prepared alumina fiber and powders. In this study, alumina precursor fiber and xerogels were prepared ...using the same aluminum carboxylate sol. The phase transformation and microstructure evolution of the precursor fibers and xerogels were investigated using TG-DSC, XRD, TEM, and SEM methods. The alumina precursor fiber and xerogels have similar chemical structures and Al(III) species. After preheated at 600 °C, most of the free water molecules, hydroxyl groups, nitrate acid radical, formic acid radicals, and acetic acid radicals are removed from the alumina precursor fiber and xerogels. The preheated fiber and xerogels exhibit amorphous phases. From the TG-DSC curves, the transformation temperature from γ-Al
2
O
3
to α-Al
2
O
3
in the preheated fiber is 30 °C lower than that in the preheated xerogels. The TEM results suggest that the fiber calcined at 1000 °C for 1 h can be completely transformed into α-Al
2
O
3
phase, while the xerogels need to be calcined at 1100 °C for 1 h to completely convert into the α-Al
2
O
3
phase. The difference in the phase transformation of the alumina fiber and xerogels was discussed in this paper.
Highlights
Alumina precursor fiber and xerogels were prepared using the same aluminum carboxylate sol.
The alumina precursor fiber and xerogels have similar chemical structures and Al(III) species.
The preheated fiber and xerogels exhibit amorphous phases.
The proportion of AlO6 units in the preheated fiber is higher than that in the preheated xerogels.
The transition temperature from γ- to α-Al
2
O
3
in the preheated fiber is 30 °C lower than the other.
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Hexavalent chromium Cr (VI) is an important environmental pollutant and may cause lung injury when inhaled into the human body. Cr (VI) is genotoxic and can cause DNA damage, although ...the underlying epigenetic mechanisms remain unclear. To simulate the real-life workplace exposure to Cr (VI), we used a novel exposure dose calculation method. We evaluated the effect of Cr (VI) on DNA damage in human bronchial epithelial cells (16HBE and BEAS-2B) by calculating the equivalent real-time exposure dose of Cr (VI) (0 to 10 μM) in an environmental population. Comet experiments and olive tail moment measurements revealed increased DNA damage in cells exposed to Cr (VI). Cr (VI) treatment increased nuclear γ-H2AX foci and γ-H2AX protein expression, and caused DNA damage in the lung tissues of mice. An effective Cr (VI) dose (6 μM) was determined and used for cell treatment. Cr (VI) exposure upregulated circ_0008657, and knockdown of circ_0008657 decreased Cr (VI)-induced DNA damage, whereas circ_0008657 overexpression had the opposite effect. Mechanistically, we found that circ_0008657 binds to microRNA (miR)-203a-3p and subsequently regulates ATM serine/threonine kinase (ATM), a key protein involved in homologous recombination repair downstream of miR-203a-3p, thereby regulating DNA damage induced by Cr (VI). The present findings suggest that circ_0008657 competitively binds to miR-203a-3p to activate the ATM pathway and regulate the DNA damage response after environmental chemical exposure in vivo and in vitro.
•BaP induces DNA damage response (DDR) in bronchial epithelial cells.•BaP upregulates circ_0057504 through suppressing DNMT3A-mediated DNA methylation.•Circ_0057504 promotes BaP-induced DDR via ...modulating NONO-SFPQ complex formation.
Benzoapyrene (BaP) is a class I carcinogen and hazardous environmental pollutant with genetic toxicity. Understanding the molecular mechanisms underlying genetic deterioration and epigenetic alterations induced by environmental contaminants may contribute to the early detection and prevention of cancer. However, the role and regulatory mechanisms of circular RNAs (circRNAs) in the BaP-induced DNA damage response (DDR) have not been elucidated. In this study, human bronchial epithelial cell lines (16HBE and BEAS-2B) were exposed to various concentrations of BaP, and BALB/c mice were treated with BaP intranasally. BaP exposure was found to induce DNA damage and upregulate circular RNA hsa_circ_0057504 (circ_0057504) expression in vitro and in vivo. In addition, BaP upregulated TMEM194B mRNA and circ_0057504 expression through inhibition of DNA methyltransferase 3 alpha (DNMT3A) expression in vitro. Modulation (overexpression or knockdown) of circ_0057504 expression levels using a lentiviral system in human bronchial epithelial cells revealed that circ_0057504 promoted BaP-induced DNA damage. RNA pull-down and western blot assays showed that circ_0057504 interacted with non-POU domain-containing octamer-binding (NONO) and splicing factor proline and glutamine rich (SFPQ) proteins and regulated formation of the NONO-SFPQ protein complex. Thus, our findings indicate that circ_0057504 acts as a novel regulator of DNA damage in human bronchial epithelial cells exposed to BaP. The current study reveals novel insights into the role of circRNAs in the regulation of genetic damage, and describes the effect and regulatory mechanisms of circ_0057504 on BaP genotoxicity.
Continuous alumina fiber exhibits excellent mechanical properties owing to its dense microstructure with fine grains. In this study, alumina fiber was prepared by the sol–gel method using iron sol as ...a nucleating agent. It was proposed that the α-Al2O3 grain size be adjusted based on the modification of colloidal particle size. The effect of holding temperature and reaction material ratio on the iron colloidal particle size was studied. The microstructure of alumina fiber was characterized by scanning electron microscopy (SEM). The experiment results indicated that iron colloidal particle size increases with the holding temperature and the NH4HCO3/Fe(NO3)3·9H2O ratio. The alumina fiber with uniform nano α-Al2O3 grains was obtained by calcination at 1400 °C for 5 min. The mean grain size tends to rise with the mean colloidal particle size. Using the iron sol as a nucleating agent, the fiber with a mean grain size of 22.5 nm could be formed. The tensile strength of fibers increased with the decrease of grain size.
Due to the lack of relevant in situ characterization techniques, the investigation of aluminum sol-gel progress is lacking. In this study, combined with molecular dynamics simulation and conventional ...experimental methods, the microstructures, rheological properties, and gelation process of the carboxylic aluminum sol system were studied. The experimental results showed that, with the increase in solid content, the microstructure of the colloid developed from a loose and porous framework to a homogeneous and compact structure. The viscosity of aluminum sol decreased significantly with the increase in temperature, and a temperature above 318 k was more conducive to improving the fluidity. The simulation results show that the increase in free volume and the connectivity of pores in colloidal framework structure were the key factors to improve fluidity. In addition, free water molecules had a higher migration rate, which could assist the rotation and rearrangement of macromolecular chains and also played an essential role in improving fluidity. The Molecular dynamics simulation (MD) results were consistent with experimental results and broaden the scope of experimental research, providing necessary theoretical guidance for enhancing the spinning properties of aluminum sol.
As a standardized vocabulary of phenotypic abnormalities associated with human diseases, the Human Phenotype Ontology (HPO) has been widely used by researchers to annotate phenotypes of ...genes/proteins. For saving the cost and time spent on experiments, many computational approaches have been proposed. They are able to alleviate the problem to some extent, but their performances are still far from satisfactory.
For inferring large-scale protein-phenotype associations, we propose HPOAnnotator that incorporates multiple Protein-Protein Interaction (PPI) information and the hierarchical structure of HPO. Specifically, we use a dual graph to regularize Non-negative Matrix Factorization (NMF) in a way that the information from different sources can be seamlessly integrated. In essence, HPOAnnotator solves the sparsity problem of a protein-phenotype association matrix by using a low-rank approximation.
By combining the hierarchical structure of HPO and co-annotations of proteins, our model can well capture the HPO semantic similarities. Moreover, graph Laplacian regularizations are imposed in the latent space so as to utilize multiple PPI networks. The performance of HPOAnnotator has been validated under cross-validation and independent test. Experimental results have shown that HPOAnnotator outperforms the competing methods significantly.
Through extensive comparisons with the state-of-the-art methods, we conclude that the proposed HPOAnnotator is able to achieve the superior performance as a result of using a low-rank approximation with a graph regularization. It is promising in that our approach can be considered as a starting point to study more efficient matrix factorization-based algorithms.
Dandelion extract is a traditional Chinese medicine and contains significant nutritional value. The aim of this study was to research the optimum fermentation conditions for dandelion addition to ...plain yogurt using a single factor experiments and orthogonal experiment. The results of the present study demonstrated that the addition of dandelion extract affected the viscosity, water-holding capacity and pH of yogurt. Optimized conditions for dandelion addition to plain yogurt based on viscosity, incubation time, pH and sensory score were 10 % sucrose, 0.3 % of the starter cultures, incubation time of 6.5 hours and 3 % dandelion extract. A new kind of dandelion yogurt with high viscosity, good water-holding capacity and good taste was prepared in this study.
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•Aerogel-like N-doped hierarchical porous carbon was prepared from corn straw.•Material with high SSA of 1871 m2/g and low density of 0.032 g/cm3 was obtained.•The maximum adsorption ...capacity of methylene blue was 1009 mg/g.•Urea addition significantly promoted the formation of adsorption sites in NHC-800.•NHC-800 exhibits good adsorption performance for various organic pollutants.
The development of green, economic and high-performance pollutant adsorption materials is an important way to meet severe environmental challenges. Herein, aerogel-like N-doped hierarchical porous carbon materials (NHCs) were prepared by rapid pyrolysis of corn straw and urea using KHCO3 as the activator. A series of characterizations including SEM, (HR)TEM, N2 absorption and desorption, FTIR, Raman, XPS, and elemental analysis were carried out to explore influences of activation temperature on the physicochemical properties of NHCs. It is found that NHC-800 prepared at 800 °C has a well-developed hierarchical pore structure, a high specific surface area (1871 m2/g) and a very low density (0.032 g/cm3). Influences of various parameters including activation temperature, urea and KHCO3 ratio, biomass type on the NHC adsorption performance were investigated. The material naming NHC-800 prepared from corn straw (corn straw: KHCO3: urea is 1:4:1) has the best methylene blue adsorption performance, with a maximum adsorption capacity of 1009.6 mg/g. Adsorption kinetics and thermodynamic analysis were carried out, and mechanism research was performed. It is found that urea not only provides pyridinic N chemisorbent sites, but also provides more activable sites for NHCs to generate more pore structures for physical adsorption. Performances on the adsorption of acid fuchsin, methyl orange, tetracycline, Cr6+, Cu2+ and actual wastewater were also studied, and it is found that NHC-800 can selectively and effectively remove organic pollutants while retaining metal ions.
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated ...with multiple gene ontology terms as its labels. Based on our GOLabeler-a state-of-the-art method for the third critical assessment of functional annotation (CAFA3), in this paper we propose NetGO, a web server that is able to further improve the performance of the large-scale AFP by incorporating massive protein-protein network information. Specifically, the advantages of NetGO are threefold in using network information: (i) NetGO relies on a powerful learning to rank framework from machine learning to effectively integrate both sequence and network information of proteins; (ii) NetGO uses the massive network information of all species (>2000) in STRING (other than only some specific species) and (iii) NetGO still can use network information to annotate a protein by homology transfer, even if it is not contained in STRING. Separating training and testing data with the same time-delayed settings of CAFA, we comprehensively examined the performance of NetGO. Experimental results have clearly demonstrated that NetGO significantly outperforms GOLabeler and other competing methods. The NetGO web server is freely available at http://issubmission.sjtu.edu.cn/netgo/.
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