Prediction of Inter-residue Multiple Distances and Exploration of Protein Multiple Conformations by Deep Learning.

AlphaFold2 has achieved a major breakthrough in end-to-end prediction for static protein structures. However, protein conformational change is considered to be a key factor in protein biological function. Inter-residue multiple distances prediction is of great significance for research on protein multiple conformations exploration. In this study, we proposed an inter-residue multiple distances prediction method, DeepMDisPre, based on an improved network which integrates triangle update, axial attention and ResNet to predict multiple distances of residue pairs. We built a dataset which contains proteins with a single structure and proteins with multiple conformations to train the network. We tested DeepMDisPre on 114 proteins with multiple conformations. The results show that the inter-residue distance distribution predicted by DeepMDisPre tends to have multiple peaks for flexible residue pairs than for rigid residue pairs. On two cases of proteins with multiple conformations, we modeled the multiple conformations relatively accurately by using the predicted inter-residue multiple distances. In addition, we also tested the performance of DeepMDisPre on 279 proteins with a single structure. Experimental results demonstrate that the average contact accuracy of DeepMDisPre is higher than that of the comparative method. In terms of static protein modeling, the average TM-score of the 3D models built by DeepMDisPre is also improved compared with the comparative method. The executable program is freely available at https://github.com/iobio-zjut/DeepMDisPre.

Preparation and Support Effect of Graphdiyne Nanotubes with Abundant Cu Quantum Dots.

Graphdiyne (GDY) is considered a very attractive support for metal nanocatalysts due to its unique structure and superior properties. The metal-GDY interaction can significantly affect the performance of catalysts. Herein, GDY nanotubes abundant in in situ formed Cu quantum dots (QDs) (Cu-GDYNT) are prepared using the electrospun polyacrylonitrile nanofibers collected on the surface of electrolytic Cu foil as templates. The diameter of the Cu-GDYNT is controllable and the uniform size of the embedded Cu QDs is about 2.2 nm. And then, the uniformly dispersed and highly active supported catalysts of ruthenium nanoparticles (Rux/Cu-GDYNT) are produced using the Cu-GDYNT as the support. Among them, the Ru3/Cu-GDYNT exhibit outstanding HER performance at all pH levels. Only 17, 67 and 83 mV overpotential is required to reach a current density of 10 mA cm-2 in 1.0 M KOH, 0.5 M H2SO4 and 1.0 M neutral PBS solutions, respectively. The sample exhibits 3000 CV cycle stability and 20 h continuous electrolysis without performance degradation in an alkaline medium. This work provides a new idea for constructing the GDY-supported metal nanocatalysts.

FSCN1 promotes proliferation, invasion and glycolysis via the IRF4/AKT signaling pathway in oral squamous cell carcinoma.

BACKGROUND: Oral squamous cell carcinoma (OSCC) is a disease with increasing incidence worldwide that leads to deformity and death. In OSCC, fascin actin-bundling protein 1 (FSCN1) is an oncogene involved in the tumorigenesis process. However, the functions and potential mechanisms of FSCN1 in the OSCC tumorigenesis process have not been reported thus far. METHODS: We used qRT‒PCR to detect the expression of FSCN1 in 40 paired OSCC tumor tissues (tumor) and neighboring noncancerous tissues. The role of FSCN1 was also assessed in vitro through colony formation, CCK-8, and transwell assays. Moreover, glucose consumption was detected. Western blotting was used to confirm the interaction of FSCN1, IRF4 and AKT. RESULTS: FSCN1 was remarkably overexpressed in OSCC tissues and cell lines compared to corresponding controls. In addition, colony formation, CCK-8, and transwell assays revealed a notable reduction in OSCC growth and invasion when FSCN1 was silenced. FSCN1 silencing remarkably suppressed OSCC glycolysis. Mechanistic studies showed that FSCN1 achieves its function partially by activating interferon regulatory factor 4 (IRF4) and the AKT pathway in OSCC. CONCLUSION: In conclusion, our study investigated the functions and mechanisms of the FSCN1/IRF4/AKT pathway in OSCC progression. In OSCC, FSCN1 is likely to be a biomarker and therapeutic target.

Comparative analysis of Fenghuang Dancong, Tieguanyin, and Dahongpao teas using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry and chemometric methods.

Fenghuang Dancong, Tieguanyin, and Dahongpao teas are belonged to semi-fermented oolong teas and are famous for their unique aroma. However, reports regarding the systematic comparison, differentiation, and classification of the volatile components of these three types of oolong teas are lacking. In this study, we aimed to establish a method for distinguishing these three types of oolong teas. The volatile components in a total of 21 tea samples of these three types of oolong teas were extracted, determined, and identified by headspace solid-phase microextraction (HS-SPME) combined with gas chromatography-mass spectrometry (GC-MS). In addition, chemometric methods such as hierarchical cluster analysis (HCA), principal component analysis (PCA), and orthogonal partial least squares discriminant analysis (OPLS-DA) were used for distinguishing and classifying the three types of oolong teas on the basis of the similarities and differences in the volatile components. The results showed that 125 volatile components were extracted and identified from the three types of oolong teas, among which 53 volatile components overlapped among the samples. The results of HCA indicated that the samples of each of the three types of oolong teas could be placed in one category when the t value was 220. The results of PCA and OPLS-DA showed that the volatile components such as dehydrolinalool, linalool oxide II, linalool, α-farnesene, linalool oxide I, ß-ocimene, nerolidol, cis-3-butyric acid folate, myrcene, and (Z)-hexanoic acid-3-hexenyl ester are the characteristic components, which can be used to distinguish the three types of oolong teas. We developed a simple, fast, and efficient method for distinguishing three types of oolong teas and provided a feasible technique for the identification of oolong tea types.

The therapeutic effect of Fufang Zhenshu Tiaozhi (FTZ) on osteoclastogenesis and ovariectomized-induced bone loss: evidence from network pharmacology, molecular docking and experimental validation.

Fufang Zhenshu Tiaozhi (FTZ) has been widely used in clinical practice and proven to be effective against aging-induced osteoporosis in mice. This study aimed to explore the mechanism of FTZ against osteoclastogenesis and ovariectomized-induced (OVX) bone loss through the network pharmacology approach. The ingredients of FTZ were collected from the previous UPLC results, and their putative targets were obtained through multiple databases. Differentially expressed genes (DEGs) during osteoclastogenesis were identified through multi-microarrays analysis. The common genes between FTZ targets and DEGs were used to perform enrichment analyses through the clusterProfier package. The affinity between all FTZ compounds and enriched genes was validated by molecular docking. The effects of FTZ on osteoclastogenesis and bone resorption were evaluated by TRAP staining, bone resorption assay and RT-qPCR in vitro, while its effects on bone loss by ELISA and Micro-CT in vivo. Enrichment analyses indicated that the inhibitory effects of FTZ may primarily involve the regulation of inflammation, osteoclastogenesis, as well as TNF-α signaling pathway. 130 pairs docking results confirmed FTZ ingredients have good binding activities with TNF-α pathway enriched genes. FTZ treatment significantly reduced TRAP, TNF-α, IL-6 serum levels and increased bone volume in OVX mice. Consistently, in vitro experiments revealed that FTZ-containing serum significantly inhibited osteoclast differentiation, bone resorption, and osteoclast related mRNA expression. This study revealed the candidate targets of FTZ and its potential mechanism in inhibiting osteoclastogenesis and bone loss induced by OVX, which will pave the way for the application of FTZ in the postmenopausal osteoporosis treatment.

Assessment of tantalum nanoparticle-induced MC3T3-E1 proliferation and underlying mechanisms.

OBJECTIVE: In our previous study, tantalum nanoparticle (Ta-NPs) was demonstrated to promote osteoblast proliferation via autophagy induction, but the specific mechanism remains unclear. In the present study, we will explore the potential mechanism. METHODS: Ta-NPs was characterized by transmission electron microscopy, scanning electron microscopy, dynamic light scattering, and BET specific surface area test. MC3T3-E1 were treated with 0 or 20 µg/mL Ta-NPs with or without pretreatment with 10 µM LY294002, Triciribine, Rapamycin (PI3K/Akt/mTOR pathway inhibitors) for 1 h respectively. Western blotting was used to detect the expressions of pathway proteins and LC3B. CCK-8 assay was used to assess cell viability. Flow cytometry was used to detect apoptosis and cell cycle. RESULTS: After pretreatment with LY294002, Triciribine and Rapamycin, the p-Akt/Akt ratio of pathway protein in Triciribine and Rapamycin groups decreased (P < 0.05), while the autophagy protein LC3-II/LC3-I in the Rapamycin group was upregulated obviously (P < 0.001). In all pretreated groups, apoptosis was increased (LY294002 group was the most obvious), G1 phase cell cycle was arrested (Triciribine and Rapamycin groups were more obvious), and MC3T3-E1 cells were proliferated much more (P < 0.01, P < 0.001, P < 0.05). CONCLUSION: Pretreatment with Triciribine or Rapamycin has a greater effect on pathway protein Akt, cell cycle arrest, autophagy protein, and cell proliferation but with inconsistent magnitude, which may be inferred that the Akt/mTOR pathway, as well as its feedback loop, were more likely involved in these processes.

Identification and similarity analysis of aroma substances in main types of Fenghuang Dancong tea.

Fenghuang Dancong tea covers the oolong tea category and is widely acknowledged for its unique floral and honey flavor. In order to characterize the volatile components in nine different aroma types of Fenghuang Dancong tea, the Headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC- MS) were employed. In addition, the similarity analysis and cluster analysis (CA) were performed to compare the aroma characteristics and establish the correlation between the nine types of teas. The principal component analysis (PCA) and orthogonal partial least squares discrimination analysis (OPLS-DA) method were employed to determine the volatile components with a high contribution to the overall aroma of each type of tea. The results presented a total of 122 volatile aroma components including 24 kinds of alcohol, 23 kinds of esters, 15 kinds of olefins, 12 kinds of aldehydes, 12 kinds of ketones, 13 kinds of alkanes and 23 kinds of other components from the nine types of Fenghuang Dancong tea. Of these volatile aroma components, 22 types were common with linalool, dehydrolinalool, linalool oxide I, linalool oxide II, etc. The similarity of the nine types of Fenghuang Dancong tea was found between 46.79% and 95.94%. The CA indicated that the nine types of Fenghuang Dancong tea could be clustered into four categories when the ordinate distance reached to 10. The PCA demonstrated that decane, octadecane, 2,2,4,6,6-pentamethylheptane, dehydrolinalool, geraniol and nerol were the important aroma components to Fenghuang Dancong Tea. OPLS-DA proved that 2,2,4,6,6-pentamethylheptane, dehydrolinalool, phenylacetaldehyde, nerolidol, linalool oxide I and hexanal were the key differential compounds between the various types of tea samples. This study provides a theoretical basis for characterizing the volatile aroma components in the main types of Fenghuang Dancong tea as well as the similarity and correlation between various types of Fenghuang Dancong tea.

Loop Enhanced Conformational Resampling Method for Protein Structure Prediction.

Protein structure prediction has been a long-standing problem for the past decades. In particular, the loop region structure remains an obstacle in forming an accurate protein tertiary structure because of its flexibility. In this study, Rama torsion angle and secondary structure feature-guided differential evolution named RSDE is proposed to predict three-dimensional structure with the exploitation on the loop region structure. In RSDE, the structure of the loop region is improved by the following: loop-based cross operator, which interchanges configuration of a randomly selected loop region between individuals, and loop-based mutate operator, which considers torsion angle feature into conformational sampling. A stochastic ranking selective strategy is designed to select conformations with low energy and near-native structure. Moreover, the conformational resampling method, which uses previously learned knowledge to guide subsequent sampling, is proposed to improve the sampling efficiency. Experiments on a total of 28 test proteins reveals that the proposed RSDE is effective and can obtain native-like models.

Effects of plant growth regulators (DA-6 and 6-BA) and EDDS chelator on phytoextraction and detoxification of cadmium by Amaranthus hybridus Linn.

In this study, pot experiments were carried out to investigative the effects of growth-promoting hormone diethyl aminoethyl hexanoate (DA-6), 6-Benzylaminopurine (6-BA), and chelator [S,S]-Ethylenediaminedisuccinic acid (EDDS) when applied to soil contaminated with cadmium (Cd). The substances were applied alone and in combination to assess their impact on biomass, Cd phytoextraction, subcellular distribution, and chemical forms in Cd hyperaccumulator Amaranthus hybridus Linn. (A. hybridus). Results showed that the treatment of EDDS alone inhibited plant growth, and raised the Cd concentration in the plant shoot and root. Treatments with DA-6 and 6-BA combined with EDDS alleviated the negative effect of EDDS on plant growth, resulting in a synergistic effect on Cd phytoaccumulation and translocation. At the subcellular level, DA-6 and 6-BA detoxified the Cd toxicity in the plant by retaining the Cd in the cell wall. On the distribution of the chemical form of Cd in plant shoot, DA-6 and 6-BA significantly decreased Cd mobility in the plant compared to EDDS. These results confirmed that combining DA-6 and 6-BA with EDDS can counteract the adverse effect of EDDS on plant growth. The treatment of 5.0 mmol kg-1 EDDS + 1 µM DA-6 was optimal for improving the remediation of A. hybridus Linn. growing in Cd contaminated soil.

A rapid and sensitive UHPLC-MS/MS method for quantification of 83b1 in plasma and its application to bioavailability study in rats.

Great attentions have been drawn by quinoline for its broad bioactivity as anti-fungal, anti-bacterial and anti-tumor activities. Compared with cisplatin, 83b1, a quinoline derivative, showed equal activity in anti-tumor and lower cyctotoxicity in normal cell. In this study, a simple, rapid and sensitive method for determination of 83b1 in rat plasma using UHPLC-MS/MS was developed for the first time. Loratadine was used as an internal standard (IS). Separation was performed on an Xterra MS C18 column by isocratic elution using acetonitrile: water solution with 1‰ formic acid (90:10, v/v) as mobile phase at a flow rate of 0.3mL/min. A triple quadrupole mass spectrometer operating in the positive ion-switching electron spray ionization mode with selection reaction monitoring (SRM) was employed to determine 83b1 and IS transitions of m/z 321.82→147.84, 382.71→258.76 for 83b1 and Loratadine, respectively. The values of specificity, linearity and lower limit of quantification, intra- and inter- day precision and accuracy, extraction recovery, matrix effect and stability for this method satisfied the acceptable limits. The lower limit of quantification was 0.5ng/mL with a linear range of 0.5-1500ng/mL. The validated method was employed to study the bioavailability of 83b1 in rat by dosing with intravenous injection (1mg/kg) and gavage (10mg/kg), and the oral bioavailability of 83b1 in rat was calculated as 20.9±8.8%.

Determination of a novel Aurora-A (AurA) kinase AKI603 by UPLC-MS/MS and its application to a bioavailability study in rat.

A simple, sensitive and accurate ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the determination of AKI603 in rat plasma has been firstly developed and validated. After a simple liquid-liquid extraction (LLE) with ethyl acetate, the analytes were separated on C18 column (2.1×100mm, 1.9µm, Thermo) by gradient elution with mobile phase of water (A) (containing 5mM ammonium acetate and 0.1% formic acid) and methanol (B) with a flow rate of 0.3mLmin(-1) and then analyzed by mass spectrometry in the positive multiple reactions monitoring (MRM) mode. The mass transitions monitored were m/z 410.0→352.9, m/z 457.1→367.9 for AKI603 and internal standard (Ly-7z), respectively. The developed method was validated for specificity, linearity and lower limit of quantification, intra- and inter-day precision and accuracy, extraction recovery, matrix effect and stability whose values satisfied the acceptable limits. The calibration curves for AKI603 was linear in concentration ranges of 0.025-5000ngmL(-1). The method has been successfully used to the bioavailability study of AKI603 administered to rats intravenously (2.5mg/kg) or orally (25mg/kg). The oral bioavailability of AKI603 in rats was calculated as 28.7±9.7%.

The Activation of NF-κB in Infiltrated Mononuclear Cells Negatively Correlates with Treg Cell Frequency in Oral Lichen Planus.

Oral lichen planus (OLP) is a T cell-mediated chronic inflammatory mucosal disease with persistent accumulation of T cells in the lamina propria. Nuclear factor-kappa B (NF-κB) is a major regulator of immune responses, and NF-κB-dependent cytokines and pro-inflammatory mediators can be detected in higher levels in the saliva and serum from patients with OLP. CD4(+)CD25(+)Foxp3(+) regulatory T (Treg) cells play an important role in the prevention of autoimmune pathology by regulating the immune response. To explore the correlation between NF-κB p65 activation and accumulation of Treg cells in patients with OLP, 40 ethnic Chinese patients with OLP and 10 healthy volunteers were recruited. The nuclear expression of NF-κB p65 in infiltrated mononuclear cells and Treg cells in the OLP lesion and the normal oral mucosa (NOM) was analyzed by immunohistochemistry assay. Our results showed that both the nuclear expression of NF-κB p65 and the number of Foxp3(+) Treg were higher in the OLP lesions. Furthermore, the frequency of Treg cells was negatively correlated with NF-κB nuclear expression in subepithelial lymphocytic infiltrate of the OLP lesion. This finding provides a new insight into the pathogenesis of OLP and may contribute to novel therapeutic strategies for the treatment of OLP by modulating the immune system.

Insulin autoantibody could help to screen latent autoimmune diabetes in adults in phenotypic type 2 diabetes mellitus in Chinese.

Latent autoimmune diabetes in adults (LADA) is characterized by a relatively mild diabetes onset, autoantibody positivity, and eventual requirement for insulin therapy. Glutamic acid decarboxylase autoantibodies (GADA) or cytoplasmic islet cell autoantibodies (ICA) play a key role in distinguishing LADA from type 2 diabetes mellitus (T2DM) in clinical practice. The aim of our research was to determine whether insulin autoantibody (IAA) has some additional value in diagnosing LADA. We analyzed IAA, GADA, and IA-2A (antibodies to insulinoma-associated antigen-2) in 1,003 newly diagnosed phenotypic T2DM patients, 110 type 1 diabetes mellitus (T1DM) patients, and 317 normal controls to survey the prevalence of IAA in phenotypic T2DM patients and the overlapping positivity of IAA with other autoantibodies. Sera were drawn within 7 days from the start of insulin therapy. Results showed that 3.39% of the newly diagnosed phenotypic T2DM, 0.95% of normal control (χ(2) = 5.3, P < 0.05), and 21.82% of T1DM (χ(2) = 68.2, P < 0.001) were positive for IAA at diagnosis. The combination frequency of three antibodies was 10.47%, which was higher than any single antibody testing. Combination testing of IAA with GADA and IA-2A could improve LADA diagnose rate by 2.39% than that of GADA and IA-2A. IAA-positive subjects had diabetes family history more common compared to its matched group (67.6% vs. 14.7%, P = 0.000). Postprandial C-peptide in IAA-positive group tended to be lower, but the difference was not statistically significant (P = 0.084). We concluded that IAA can be used to screen LADA in phenotypic T2DM in the Chinese population.

[Morsicatio buccarum et labiorum: two cases report].

Morsicatio buccarum et labiorum is a form of chronic oral mucosa disease caused by habitual cheek or lip biting. The affected mucosa shows a shredded appearance. The patients may feel their oral mucosa rough. In present, there have not been unified denomination and systematic introduction about this disease in our country. Two cases were reported here. The pathogenesis, clinical manifestation, pathology, diagnosis, differential diagnosis, treatment and prognosis about this disease were also discussed.

[The oral exosyndrome and diagnosis of 3 patients with acquired immune deficiency syndrome].

The aim of the report is to increase the dentists', vigilance to the acquired immune deficiency syndrome (AIDS) by means of analyzing the oral exosyndrome and discussing the experience of diagnosis to 3 patients with AIDS. Vigilance to AIDS can make us to discover, diagnose and treat it in the early stage, and prevent us from transmission of the disease.

[Purification and activity calculated of fibrinolyric factors from Eupolyphaga sinensis].

Three kinds ( EFF-1, EFF-2 and EFF-3) of fibrinolytic factor were separated by ammonium sulphate precipitation, DEAE-cellulose and preparative PAGE electrophoresis from female Eupolyphaga sinensis Walker. Their molecular weights were proved to be 41kd, 32.9 kd and 30.6 kd respectively with SDS-PAGE electophoresis. Their Activities as plasminogen activator were 171.3 U/mg, 234.0 U/mg and 148.5 U/mg. In addition, EFF-2 and EFF-3 were not only fibrinolytic activities but also have plasminogen activator on fibrinous plate lacked of plasminogen . There had been no such components of plasminogen activator and fiberinolytic enzyme from Eupolyphaga sinensis reported yet.

[Purification and biochemical character of a fibrinolytic protein from Eupolyphaga sinensis].

A novel of fibrinolytic protein has been separated and purified by ammonium sulfate fractionation, DEAE-cellulose and SephadexG-75 Column chromatography from the tissue of the female Eupolyphaga sinensis in the paper. The protein showed an apparent molecular weight of 41.3 kD on sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. In addition, it includes 10.5% sugar. Its specific activity to hydrolyze fibrin was 547.86 u/mg. The enzyme activity was inhibited by Mg2+, Ca2+, protein inhibitors, such as 8mol/L urea and 1% beta-mercaptoethanol, and serine protease inhibitor such as phenylmethanesulfonyl fluoride (PMSF), but wasn't inhibited by Na+, K+ and ethylenediaminotetraacetic acid (EDTA). The protein was stable under 40 degrees C and it's optimal temperature was also 40 degrees C. It's optimal pH was 8.0. It showed a different way between the activity and UK when they degrade the plasminogen. Based on all the messages the protein can be suggested to be a novel fibrinolytic protein. There have been no such component of fiberinolytic enzyme from Eupolyphaga sinensis walker reported yet.