Calculation of solvation force in molecular dynamics simulation by deep-learning method.

Electrostatic calculations are generally used in studying the thermodynamics and kinetics of biomolecules in solvent. Generally, this is performed by solving the Poisson-Boltzmann equation on a large grid system, a process known to be time consuming. In this study, we developed a deep neural network to predict the decomposed solvation free energies and forces of all atoms in a molecule. To train the network, the internal coordinates of the molecule were used as the input data, and the solvation free energies along with transformed atomic forces from the Poisson-Boltzmann equation were used as labels. Both the training and prediction tasks were accelerated on GPU. Formal tests demonstrated that our method can provide reasonable predictions for small molecules when the network is well-trained with its simulation data. This method is suitable for processing lots of snapshots of molecules in a long trajectory. Moreover, we applied this method in the molecular dynamics simulation with enhanced sampling. The calculated free energy landscape closely resembled that obtained from explicit solvent simulations.

Connexin43 overexpression promotes bone regeneration by osteogenesis and angiogenesis in rat glucocorticoid-induced osteonecrosis of the femoral head.

Glucocorticoids induced osteonecrosis of the femoral head (GIONFH) is a devastating orthopedic disease. Previous studies suggested that connexin43 is involved in the process of osteogenesis and angiogenesis. However, the role of Cx43 potentiates in the osteogenesis and angiogenesis of bone marrow-derived stromal stem cells (BMSCs) in GIONFH is still not investigated. In this study, BMSCs were isolated and transfected with green fluorescent protein or the fusion gene encoding GFP and Cx43. The osteogenic differentiation of BMSCs were detected after transfected with Cx43. In addition, the migration abilities and angiogenesis of human umbilical vein endothelial cells (HUVECs) were been detected after induced by transfected BMSCs supernatants in vitro. Finally, we established GC-ONFH rat model, then, a certain amount of transfected or controlled BMSCs were injected into the tibia of the rats. Immunohistological staining and micro-CT scanning results showed that the transplanted experiment group had significantly promoted more bone regeneration and vessel volume when compared with the effects of the negative or control groups. This study demonstrated for the first time that the Cx43 overexpression in BMSCs could promote bone regeneration as seen in the osteogenesis and angiogenesis process, suggesting that Cx43 may serve as a therapeutic gene target for GIONFH treatment.

Resistance mechanism of Phomopsis longicolla to fludioxonil is associated with modifications in PlOS1, PlOS4 and PlOS5.

Phomopsis longicolla, a causal agent of soybean root rot, stem blight, seed decay, pod and stem canker, which seriously affects the yield and quality of soybean production worldwide. The phenylpyrrole fungicide fludioxonil exhibits a broad spectrum and high activity against phytopathogenic fungi. In this study, the baseline sensitivity of 100 P. longicolla isolates collected from the main soybean production areas of China to fludioxonil were determined. The result showed that the EC50 values of all the P. longicolla isolates ranged from 0.013 to 0.035 µg/ml. Furthermore, 12 fludioxonil-resistance (FluR) mutants of P. longicolla were generated from 6 fludioxonil-sensitive (FluS) isolates. and the resistance factors (RF) of 12 FluR mutants were >3500. Sequence alignment showed that multiple mutation types were found in PlOS1, PlOS4 or/and PlOS5 of FluR mutants. All the FluR mutants exhibited fitness penalty in mycelial growth, conidiation, virulence and osmo-adaptation. Under fludioxonil or NaCl treatment condition, the glycerol accumulation was significantly increased in FluS isolates, but was slightly increased in FluR mutants, and the phosphorylation level of most FluR mutants was significantly decreased when compared to the FluS isolates. Additionally, positive cross-resistance was observed between fludioxonil and procymidone but not fludioxonil and pydiflumetofen, pyraclostrobin or fluazinam. This is first reported that the baseline sensitivity of P. longicolla to fludioxonil, as well as the biological and molecular characterizations of P. longicolla FluR mutants to fludioxonil. These results can provide scientific directions for controlling soybean diseases caused by P. longicolla using fludioxonil.

Crucial Involvement of Heme Biosynthesis in Vegetative Growth, Development, Stress Response, and Fungicide Sensitivity of Fusarium graminearum.

Heme biosynthesis is a highly conserved pathway from bacteria to higher animals. Heme, which serves as a prosthetic group for various enzymes involved in multiple biochemical processes, is essential in almost all species, making heme homeostasis vital for life. However, studies on the biological functions of heme in filamentous fungi are scarce. In this study, we investigated the role of heme in Fusarium graminearum. A mutant lacking the rate-limiting enzymes in heme synthesis, coproporphyrinogen III oxidase (Cpo) or ferrochelatase (Fc), was constructed using a homologous recombination strategy. The results showed that the absence of these enzymes was lethal to F. graminearum, but the growth defect could be rescued by the addition of hemin, so we carried out further studies with the help of hemin. The results demonstrated that heme was required for the activity of FgCyp51, and its absence increased the sensitivity to tebuconazole and led to the upregulation of FgCYP51 in F. graminearum. Additionally, heme plays an indispensable role in the life cycle of F. graminearum, which is essential for vegetative growth, conidiation, external stress response (especially oxidative stress), lipid accumulation, fatty acid ß-oxidation, autophagy, and virulence.

Enhanced sampling in explicit solvent by deep learning module in FSATOOL.

FSATOOL is an integrated molecular simulation and data analysis program. Its old molecular dynamics engine only supports simulations in vacuum or implicit solvent. In this work, we implement the well-known smooth particle mesh Ewald method for simulations in explicit solvent. The new developed engine is runnable on both CPU and GPU. All the existed analysis modules in the program are compatible with the new engine. Moreover, we also build a complete deep learning module in FSATOOL. Based on the module, we further implement two useful trajectory analysis methods: state-free reversible VAMPnets and time-lagged autoencoder. They are good at searching the collective variables related to the conformational transitions of biomolecules. In FSATOOL, these collective variables can be further used to construct a bias potential for the enhanced sampling purpose. We introduce the implementation details of the methods and present their actual performances in FSATOOL by a few enhanced sampling simulations.

SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules.

In this work, we present SurfPB as a useful tool for the study of biomolecules. It can do many typical calculations, including the molecular surface, electrostatic potential, solvation free energy, entropy, and binding free energy. Among all of the calculations, the entropy calculation is the most time-consuming one. In SurfPB, the calculation can be performed in a vacuum or implicit solvent and accelerated on GPU. The Poisson-Boltzmann equation solver is accelerated on GPU as well. Moreover, we developed a graphical user interface for SurfPB. It allows users to input the parameters and complete the whole calculation in a visual way. The calculated electrostatic potentials are shown on the molecular surface in a three-dimensional scene.

Phenamacril and carbendazim regulate trichothecene mycotoxin synthesis by affecting ROS levels in F. asiaticum.

Fusarium head blight caused by Fusarium asiaticum is an important cereal crop disease, and the trichothecene mycotoxins produced by F. asiaticum can contaminate wheat grain, which is very harmful to humans and animals. To effectively control FHB in large areas, the application of fungicides is the major strategy; however, the application of different types of fungicides has varying influences on the accumulation of trichothecene mycotoxins in F. asiaticum. In this study, phenamacril inhibited trichothecene mycotoxin accumulation in F. asiaticum; however, carbendazim (N-1H-benzimidazol-2-yl-carbamic acid, methyl ester) induced trichothecene mycotoxin accumulation. Additionally, phenamacril led to a lower level of reactive oxygen species (ROS) by inducing gene expression of the catalase and superoxide dismutase (SOD) pathways in F. asiaticum, whereas carbendazim stimulated ROS accumulation by inhibiting gene expression of the catalase and SOD pathways. Based on these results, we conclude that phenamacril and carbendazim regulate trichothecene mycotoxin synthesis by affecting ROS levels in F. asiaticum.

Intravertebral insertion of interbody fusion cage via transpedicular approach for the treatment of stage III Kümmell disease: a technical note and case presentation.

BACKGROUND: Kümmell disease usually occurs in the elderly osteoporosis population and develops gradually into symptomatic, progressive kyphosis of the spine. However, current surgical methods to deal with stage III Kümmell disease are less satisfying. The objective of this study was to describe a less invasive technique for treating stage III Kümmell disease. TECHNIQUE: A less invasive technique of intravertebral insertion of interbody fusion cage via transpedicular approach with posterior spine stabilization was applied to treat stage III Kümmell disease. RESULTS: This study details a modified technique applied in a patient with stage III Kümmell disease, showing significant improvement in pain relief, anterior column height recovery, and kyphotic angle correction. And no complications were reported during our follow-up. CONCLUSIONS: Intravertebral insertion of interbody fusion cage via transpedicular approach provides advantages of acceptable correction of kyphosis, bony fusion, minimal invasion. Thus, our method was a good alternative choice for stage III Kümmell disease.

Does living at high altitude increase the risk of bleeding events after total knee arthroplasty? A retrospective cohort study.

OBJECTIVE: Post-operative bleeding after total knee arthroplasty (TKA) is a frequent cause of post-operative complications. This study compared blood loss and indicators of coagulation and fibrinolysis between TKA patients living at low or high altitudes. METHODS: We retrospectively analyzed 120 patients at our institution who underwent primary TKA from May 2019 to March 2020, and we divided them into those living in areas about 500 m or > 3000 m above sea level. We compared the primary outcome of total blood loss between them. We also compared them in terms of several secondary outcomes: coagulation and fibrinolysis parameters, platelet count, reduction in hemoglobin, hidden blood loss, intra-operative blood loss, transfusion rate, and incidence of thromboembolic events and other complications. RESULTS: Total blood loss was significantly higher in the high-altitude group than in the low-altitude group (mean, 748.2 mL [95% CI, 658.5-837.9] vs 556.6 mL [95% CI, 496.0-617.1]; p = 0.001). The high-altitude group also showed significantly longer activated partial thromboplastin time, prothrombin time, and thrombin time before surgery and on post-operative day one, as well as increased levels of fibrinogen/fibrin degradation product on post-operative days one and three. Ecchymosis was significantly more frequent in the high-altitude group (41.7 vs 21.7%; relative risk (RR) = 1.923 [95% CI, 1.091-3.389]; p = 0.019). The two groups showed similar transfusion rates, and none of the patients experienced venous thromboembolism, pulmonary embolism, or infection. CONCLUSION: High altitude may alter coagulation and fibrinolysis parameters in a way that increases risk of blood loss after TKA. Such patients may benefit from special management to avoid bleeding events.

[Research and Application of Smartphone-based Detection System to Immunoassay].

The emergence of smart phones has not only brought extensive changes to people's way of life, but also provided a new research platform for the expansion and application of science and technology. Technicians have combined immunoassay methods with smart phone sensing technology to develop a variety of smartphone-based biological sample analysis and detection sensing systems, promoting the application of immunoassay methods in POCT fields. In this review, we summarize the researches and applications of smart-phone in the field of immune analysis. According to the different sensors and detection objects, these applications can be divided into four aspects: camera-based spectrometer, camera-based enzyme reader, camera-based strip reader and spectrophotometer based on environmental light sensor. This study also briefly discusses some limitations of current smart phone application in immune analysis, and prospects the future applicability of smart phone sensing system.

FSATOOL 2.0: An integrated molecular dynamics simulation and trajectory data analysis program.

Molecular dynamics simulation is important in the computational study of the biomolecules. In this paper, we upgrade our previous FSATOOL to version 2.0. It is no longer a plugin as before. Besides the existed enhanced sampling and Markov state model analysis module, FSATOOL 2.0 has three new features now. First, it contains a molecular dynamics simulation engine on both CPU and GPU device. The engine works with an embedded enhanced sampling module. Second, it can do the free energy calculation by various practical methods, including the weighted histogram analysis method and Gaussian mixture model. Third, it has many subroutines to process the trajectory data, such as principal component analysis, time-structure based independent component analysis, contact analysis, and Φ-value analysis. Most importantly, all these calculations are integrated into one package. The trajectory data format is compatible with all the modules. With a proper input parameter file, users can do the molecular dynamics simulation and data analysis work by only a few simplified commands. The capabilities and theoretical backgrounds of FSATOOL 2.0 are introduced in the paper.

Discovery of pyrrolo[2,3-d]pyrimidine-based molecules as a Wee1 inhibitor template.

In the past decade, Wee1 inhibition has received widespread attention as a cancer therapy. Our research aims to discover effective, selective and drug-like Wee1 inhibitors. Herein, a series of compounds with pyrrolo[2,3-d]pyrimidine-based heterocycles were designed, synthesized and confirmed to inhibit Wee1 kinase. The inhibitors afforded good potency in Wee1 Kinase inhibitory activity in enzymatic assays. These compounds showed strong proliferation inhibition against NCI-1299 cell lines and had acceptable pharmacokinetic properties. These derivatives are promising inhibitors that warrant further evaluation, towards the development of potential anticancer drug.

Diaporthe Diversity and Pathogenicity Revealed from a Broad Survey of Soybean Stem Blight in China.

Many species in the fungal Diaporthe (anamorph Phomopsis) genus have become a group of the most important pathogens that cause seed decay, stem and pot blight, and stem canker in soybean production worldwide, resulting in significant yield loss. Due to increased disease prevalence but a lack of research, we performed an extensive field survey to isolate and identify the Diaporthe species associated with soybean stem blight in six provinces of China between 2019 and 2020. A total of 92 Diaporthe isolates were identified based on morphological and multilocus phylogenetic analysis and classified into six species: D. longicolla, D. unshiuensis, D. sojae, D. caulivora, D. tectonigena, and an unknown Diaporthe sp. The most frequently identified species was D. longicolla with 57 isolates. High genetic diversity was observed for the D. longicolla isolates, and haplotype network analysis revealed a mixed structure among the population in the six provinces. In comparative pathogenicity assays, different virulence levels were observed among the 92 Diaporthe isolates. The results of this study provide new insights into the Diaporthe spp. associated with soybean stem blight in China and can help in the development of effective management strategies.

Primary cutaneous diffuse large B-cell lymphoma after total knee arthroplasty: a case study and a systematic review of its cutaneous manifestations and treatment options.

Introduction: Primary cutaneous diffuse large B-cell lymphoma (PCDLBCL) after total knee arthroplasty (TKA) is rare. Aim: The literature that analyses the cutaneous manifestations of PCDLBCL and assesses the effect and the outcome of treatment is scarce. Material and methods: We described a case of PCDLBCL after TKA, whose cutaneous mass develops around surgical sites, mimicking a prosthetic joint infection. In addition, we conducted a systematic review of 29 reported cases with PCDLBCL. Primary endpoint for the review was main cutaneous manifestations of PCDLBCL. Secondary endpoint included treatment options of PCDLBCL and optimal therapeutic method. Results: We found that the main cutaneous manifestations include infiltrative cutaneous lesions such as macules, papules or nodules, some of them presented as ulcerations or formation of vesicles, subcutaneous nodules or both. The treatment options include excision, radiotherapy, chemotherapy, and even "watchful waiting" as spontaneous regression was noted in some cases. Systemic chemotherapy is the most frequent initial treatment approach chosen, of which rituximab is often combined with cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) chemotherapy and patients who received systemic rituximab tend to have a better overall survival (OS) time than those who did not. Conclusions: PCDLBCL is a rare disease after TKA, however, an early recognition and distinguishing from infection is still needed. Patients with PCDLBCL may profit from rituximab-based chemotherapy, increasing the survival rate, despite the high relapse rate and limited OS time in some cases.

Glucocorticoids decreased Cx43 expression in osteonecrosis of femoral head: The effect on proliferation and osteogenic differentiation of rat BMSCs.

Glucocorticoid (GC)-induced osteonecrosis of the femoral head (GC-ONFH) is considered as one of the most serious side effects of long-term or over-dose steroid therapy. However, the underlying cause mechanisms are still not fully investigated. We firstly established a rat model of GC-ONFH and injected lipopolysaccharide (LPS) and methylprednisolone (MPS). We found that the expressions of Cx43, Runx2, ALP and COLⅠ were more decreased than the normal group. Secondly, the isolated rat bone marrow stem cells (BMSCs) were treated with dexamethasone (Dex) in vitro, and the expressions of Cx43, Runx2, ALP and COLⅠ were decreased significantly. Moreover, the results of immunofluorescence staining, alizarin red staining, EdU assay and CCK8 showed that the osteogenic differentiation and the proliferation capacity of BMSCs were decreased after induced by Dex. A plasmid of lentivirus-mediated Cx43 (Lv-Cx43) gene overexpression was established to investigate the function of Cx43 in BMSCs under the Dex treatment. Findings demonstrated that the proliferation and osteogenic differentiation abilities were enhanced after Lv-Cx43 transfected to BMSCs, and these beneficial effects of Lv-Cx43 were significantly blocked when PD988059 (an inhibitor of ERK1/2) was used. In conclusion, the overexpression of Cx43 could promote the proliferation and osteogenic differentiation of BMSCs via activating the ERK1/2 signalling pathway, which provide a basic evidence for further study on the detailed function of Cx43 in GC-ONFH.

Investigating the folding mechanism of the N-terminal domain of ribosomal protein L9.

Protein folding is a popular topic in the life science. However, due to the limited sampling ability of experiments and simulations, the general folding mechanism is not yet clear to us. In this work, we study the folding of the N-terminal domain of ribosomal protein L9 (NTL9) in detail by a mixing replica exchange molecular dynamics method. The simulation results are close to previous experimental observations. According to the Markov state model, the folding of the protein follows a nucleation-condensation path. Moreover, after the comparison to its 39-residue ß-α-ß motif, we find that the helix at the C-terminal has a great influence on the folding process of the intact protein, including the nucleation of the key residues in the transition state ensemble and the packing of the hydrophobic residues in the native state.

Detection and Biological Characteristics of Alternaria alternata Resistant to Difenoconazole from Paris polyphylla var. chinensis, an Indigenous Medicinal Herb.

Black spot caused by Alternaria alternata (BSAA) is one of the most common diseases of Paris polyphylla var. chinensis, causing yield losses in China. Demethylation inhibitors (DMIs) have been used to control this disease in China for decades. Some farmers have complained about the decreased efficacy of DMIs against BSAA. The objective of this study was to detect and characterize the resistance of A. alternata against difenoconazole from P. polyphylla var. chinensis during 2018. Of the 22 isolates of A. alternata obtained from Sichuan Province in the southwest of China, 20 were resistant to difenoconazole. Mycelial growth rates and sporulation of the difenoconazole-resistant (DfnR) isolates were not different from those of the difenoconazole-sensitive (DfnS) isolates. No cross resistance between difenoconazole and tebuconazole or propiconazole was observed. Mutations were identified at gene AaCYP51 of DfnR isolates based on the sequence alignment of the DfnR and DfnS isolates. All of the mutations could be divided into three resistant genotypes, I (K715R + Y781C), II (K715R + D1140G + T1628A), and III (no mutation). The docking total score of the DfnS isolates was 5.6020, higher than the resistant genotype I (4.4599) or the resistant genotype II (3.8651), suggesting that the DMI resistance of A. alternata may be caused by the decreased affinity between AaCYP51 and difenoconazole.

Detection and Fitness of Dicarboximide-Resistant Isolates of Alternaria alternata from Dendrobium officinale, a Chinese Indigenous Medicinal Herb.

Black spot, caused by Alternaria alternata, poses a severe threat to the industry of Dendrobium officinale, a Chinese indigenous medicinal herb. Dicarboximide fungicides (DCFs) have been intensively used to control this disease for decades in China, and offer excellent efficacy. The resistance of phytopathogenic pathogens against DCFs are reportedly selected in fields; however, the DCF resistance of A. alternata from D. officinale is not well understood. The isolates of A. alternata with low procymidone resistance (ProLR) were detected in the commercial orchards of D. officinale in China in 2018 and biochemically characterized in this study. The result showed that the ProLR isolates were selected in the commercial orchards with a resistance frequency of 100%, and no significant difference in mycelial growth, sporulation, and virulence was observed among the ProLR and procymidone-sensitive (ProS) isolates. A positive cross-resistance pattern was exhibited between procymidone and iprodione. Results of amino acid sequence alignment of AaOS-1 from the tested isolates showed that all of the ProLR genotypes could be categorized into two groups, including group I (mutations at AaOs-1) and group II (no mutation). Under procymidone (5.0 µg/ml) treatment conditions, the AaOs-1 expression levels increased in the ProS isolates and ranged from approximately 2.94- to 3.69-fold higher than those under procymidone-free conditions, while the AaOs-1 expressions of the ProLR isolates were significantly lower than those in the ProS isolates under the same conditions. The data indicated that the mutations at AaOs-1 are involved in the DCF resistance of A. alternata selected in the D. officinale orchards.

Biological Characteristics and Molecular Mechanism of Procymidone Resistance in Stemphylium eturmiunum From Garlic.

Garlic leaf blight caused by Stemphylium eturmiunum was first reported in Jiangsu Province in China. The dicarboximide fungicide (DCF) procymidone is reported to possess broad-spectrum action in inhibiting filamentous fungi and is widely used to control leaf disease of various plants. Of 41 Stemphylium eturmiunum isolates collected in this study from commercial garlic farms in Pizhou and Dafeng counties of Jiangsu Province, eight isolates were resistant to procymidone. The following three phenotypes were categorized according to in vitro responses to DCFs: sensitive, low resistance to iprodione and procymidone, and high resistance to all iprodione and procymidone. The fitness of all resistant isolates was decreased in accordance with data on mycelial growth, conidiation, and virulence. After treatment with 10 µg/ml of procymidone for 4 h, mycelial intracellular glycerol concentrations of resistant isolates were significantly lower than those of sensitive isolates. Positive cross-resistance was observed between dicarboximides and phenylpyrroles, but there was no cross-resistance between dicarboximides and fluazinam or difenoconazole in the two resistant phenotypes. Nucleotide sequence alignment of two-component histidine kinase genes from sensitive and resistant isolates indicated that amino acid mutations were located at the histidine kinase, adenylyl cyclase, methyl-accepting chemotaxis protein and at the phosphatase domain of the N-terminal region and the response regulator domain of the C-terminal region. To our knowledge, this is the first report of DCF resistance in Stemphylium eturmiunum, and these findings will help establish a rational strategy to manage DCF-resistant populations of Stemphylium eturmiunum in the field.

Meta-analysis of retrospective studies suggests that the pre-operative opioid use is associated with an increased risk of adverse outcomes in total hip and or knee arthroplasty.

BACKGROUND: Opioid use is prevalent in the general population. This systematic review and meta-analysis sought to evaluate whether it affects patient-reported outcomes (PROs) following total hip or knee arthroplasty. METHODS: The following databases were systematically searched on February 5, 2020: Medline, Embase (Ovid), Cochrane Library, and Web of Science. Studies were included if they compared patients who received opioids or not before total hip or knee arthroplasty. Outcomes of interest were rates of post-operative revision, peri-prosthetic infection, and readmission. RESULTS: Ten retrospective studies were included for review. Pre-operative opioid use was identified as a risk factor for post-operative revision [odds ratio (OR) 1.58, 95% confidence interval (CI) 1.15-1.73, p<0.01], peri-prosthetic infection (OR 1.36, 95% CI 1.08-1.71, p=0.01), and readmission (OR 1.41, 95% CI 1.20-1.75, p<0.01). CONCLUSION: The available evidence indicates that pre-operative opioid use increases the risk of adverse outcomes following total hip or knee arthroplasty. Orthopedic physicians should consider these risks when treating their patients.