Descriptor-augmented machine learning for enzyme-chemical interaction predictions

Descriptors play a pivotal role in enzyme design for the greener synthesis of biochemicals, as they could characterize enzymes and chemicals from the physicochemical and evolutionary perspective. This study examined the effects of various descriptors on the performance of Random Forest model used for enzyme-chemical relationships prediction. We curated activity data of seven specific enzyme families from the literature and developed the pipeline for evaluation the machine learning model performance using 10-fold cross-validation. The influence of protein and chemical descriptors was assessed in three scenarios, which were predicting the activity of unknown relations between known enzymes and known chemicals (new relationship evaluation), predicting the activity of novel enzymes on known chemicals (new enzyme evaluation), and predicting the activity of new chemicals on known enzymes (new chemical evaluation). The results showed that protein descriptors significantly enhanced the classification performance of model on new enzyme evaluation in three out of the seven datasets with the greatest number of enzymes, whereas chemical descriptors appear no effect. A variety of sequence-based and structure-based protein descriptors were constructed, among which the esm-2 descriptor achieved the best results. Using enzyme families as labels showed that descriptors could cluster proteins well, which could explain the contributions of descriptors to the machine learning model. As a counterpart, in the new chemical evaluation, chemical descriptors made significant improvement in four out of the seven datasets, while protein descriptors appear no effect. We attempted to evaluate the generalization ability of the model by correlating the statistics of the datasets with the performance of the models. The results showed that datasets with higher sequence similarity were more likely to get better results in the new enzyme evaluation and datasets with more enzymes were more likely beneficial from the protein descriptor strategy. This work provides guidance for the development of machine learning models for specific enzyme families.

Enhancing the stability of a novel D-allulose 3-epimerase from Ruminococcus sp. CAG55 by interface interaction engineering and terminally attached a self-assembling peptide

D-allulose, a highly desirable sugar substitute, is primarily produced using the D-allulose 3-epimerase (DAE). However, the availability of usable DAE enzymes is limited. In this study, we discovered and engineered a novel DAE Rum55, derived from a human gut bacterium Ruminococcus sp. CAG55. The activity of Rum55 was strictly dependent on the presence of Co2+, and it exhibited an equilibrium conversion rate of 30.6 % and a half-life of 4.5 h at 50 °C. To enhance its performance, we engineered the interface interaction of Rum55 to stabilize its tetramer structure, and the best variant E268R was then attached with a self-assembling peptide to form active enzyme aggregates as carrier-free immobilization. The half-life of the best variant E268R-EKL16 at 50 °C was dramatically increased 30-fold to 135.3 h, and it maintained 90 % of its activity after 13 consecutive reaction cycles. Additionally, we identified that metal ions played a key role in stabilizing the tetramer structure of Rum55, and the dependence on metal ions for E268R-EKL16 was significantly reduced. This study provides a useful route for improving the thermostability of DAEs, opening up new possibilities for the industrial production of D-allulose.

A comprehensive transformer-based approach for high-accuracy gas adsorption predictions in metal-organic frameworks

Gas separation is crucial for industrial production and environmental protection, with metal-organic frameworks (MOFs) offering a promising solution due to their tunable structural properties and chemical compositions. Traditional simulation approaches, such as molecular dynamics, are complex and computationally demanding. Although feature engineering-based machine learning methods perform better, they are susceptible to overfitting because of limited labeled data. Furthermore, these methods are typically designed for single tasks, such as predicting gas adsorption capacity under specific conditions, which restricts the utilization of comprehensive datasets including all adsorption capacities. To address these challenges, we propose Uni-MOF, an innovative framework for large-scale, three-dimensional MOF representation learning, designed for multi-purpose gas prediction. Specifically, Uni-MOF serves as a versatile gas adsorption estimator for MOF materials, employing pure three-dimensional representations learned from over 631,000 collected MOF and COF structures. Our experimental results show that Uni-MOF can automatically extract structural representations and predict adsorption capacities under various operating conditions using a single model. For simulated data, Uni-MOF exhibits remarkably high predictive accuracy across all datasets. Additionally, the values predicted by Uni-MOF correspond with the outcomes of adsorption experiments. Furthermore, Uni-MOF demonstrates considerable potential for broad applicability in predicting a wide array of other properties.

Exploring steric and electronic effects in tailoring lithium-ion solvation using engineered ether solvents through molecular dynamics simulations

Lithium-metal batteries, distinguished by their exceptional energy density, emerge as a viable candidate for addressing future energy storage demands. Despite this, the broader integration of lithium-metal batteries is hindered by the intrinsic instability present between lithium metal and conventional liquid lithium electrolytes, which were initially engineered for graphite anodes in lithium-ion batteries. Contemporary research highlights the critical role of electrolyte engineering in harnessing the full potential of lithium-metal batteries. A prominent strategy in this realm is the fluorination of solvent molecules, with a particular focus on those belonging to the ether category. However, achieving a holistic understanding of the myriad factors influencing the molecular design of solvents remains a challenging endeavor. In this study, we investigate four solvents synthesized from Dimethoxyethane (DME) employing molecular dynamics simulations. These solvents are methodically modified by either incorporating additional alkyl groups or through fluorination. Our analysis specifically focuses on two pivotal aspects: the steric effects induced by the integration of larger alkyl chains, and the electronic effects resulting from fluorination. We conduct an in-depth examination of the stability, ion transport properties, and solvation dynamics displayed by these novel solvents. Our findings highlight the significant influence of modifying both steric and electronic properties of solvent molecules on the solvation behavior of Li+ ions. This modification notably affects the coordination intensity and the interaction mechanism between Li+ ions and solvation sites within the first solvation shell, offering vital insights into the variations in ion transport characteristics across different electrolytes. .

Designing artificial ion channels with strict K+/Na+ selectivity toward next-generation electric-eel-mimetic ionic power generation

A biological potassium channel is >1000 times more permeable to K+ than to Na+ and exhibits a giant permeation rate of ∼108 ions/s. It is a great challenge to construct artificial potassium channels with such high selectivity and ion conduction rate. Herein, we unveil a long-overlooked structural feature that underpins the ultra-high K+/Na+ selectivity. By carrying out massive molecular dynamics simulation for ion transport through carbonyl-oxygen-modified bi-layer graphene nanopores, we find that the twisted carbonyl rings enable strict potassium selectivity with a dynamic K+/Na+ selectivity ratio of 1295 and a K+ conduction rate of 3.5 × 107 ions/s, approaching those of the biological counterparts. Intriguingly, atomic trajectories of K+ permeation events suggest a dual-ion transport mode, i.e. two like-charged potassium ions are successively captured by the nanopores in the graphene bi-layer and are interconnected by sharing one or two interlayer water molecules. The dual-ion behavior allows rapid release of the exiting potassium ion via a soft knock-on mechanism, which has previously been found only in biological ion channels. As a proof-of-concept utilization of this discovery, we propose a novel way for ionic power generation by mixing KCl and NaCl solutions through the bi-layer graphene nanopores, termed potassium-permselectivity enabled osmotic power generation (PoPee-OPG). Theoretically, the biomimetic device achieves a very high power density of >1000 W/m2 with graphene sheets of <1% porosity. This study provides a blueprint for artificial potassium channels and thus paves the way toward next-generation electric-eel-mimetic ionic power generation.

Computational design of highly efficient thermostable MHET hydrolases and dual enzyme system for PET recycling

Recently developed enzymes for the depolymerization of polyethylene terephthalate (PET) such as FAST-PETase and LCC-ICCG are inhibited by the intermediate PET product mono(2-hydroxyethyl) terephthalate (MHET). Consequently, the conversion of PET enzymatically into its constituent monomers terephthalic acid (TPA) and ethylene glycol (EG) is inefficient. In this study, a protein scaffold (1TQH) corresponding to a thermophilic carboxylesterase (Est30) was selected from the structural database and redesigned in silico. Among designs, a double variant KL-MHETase (I171K/G130L) with a similar protein melting temperature (67.58 °C) to that of the PET hydrolase FAST-PETase (67.80 °C) exhibited a 67-fold higher activity for MHET hydrolysis than FAST-PETase. A fused dual enzyme system comprising KL-MHETase and FAST-PETase exhibited a 2.6-fold faster PET depolymerization rate than FAST-PETase alone. Synergy increased the yield of TPA by 1.64 fold, and its purity in the released aromatic products reached 99.5%. In large reaction systems with 100 g/L substrate concentrations, the dual enzyme system KL36F achieved over 90% PET depolymerization into monomers, demonstrating its potential applicability in the industrial recycling of PET plastics. Therefore, a dual enzyme system can greatly reduce the reaction and separation cost for sustainable enzymatic PET recycling.

A Remineralizing and Antibacterial Coating for Arresting Caries

Dental caries is a dynamic disease induced by the unbalance between demineralization of dental hard tissues caused by biofilm and remineralization of them; however, although various effective remineralization methods have been well documented, it is a challenge to reestablish the balance by enhancing remineralization alone while ignoring the antibacterial therapy. Therefore, the integration of remineralizing and antibacterial technologies offers a promising strategy to halt natural caries progression in clinical practice. Here, the conception of interrupting dental caries (IDC) was proposed based on the development of dual-functional coating with remineralizing and antibacterial properties. In this study, bovine serum albumin (BSA) loaded octenidine (OCT) successfully to form a BSA-OCT composite. Subsequently, through fast amyloid-like aggregation, the phase-transited BSA-OCT (PTB-OCT) coating can be covered on teeth, resin composite, or sealant surfaces in 30 min by a simple smearing process. The PTB-OCT coating showed satisfactory effects in promoting the remineralization of demineralized enamel and dentin in vitro. Moreover, this coating also exerted significant acid-resistance stability and anti-biofilm properties. Equally importantly, this coating exhibited promising abilities in reducing the microleakage between the tooth and resin composite in vitro and preventing primary and secondary caries in vivo. In conclusion, this novel dual-functional PTB-OCT coating could reestablish the balance between demineralization and remineralization in the process of caries, thereby potentially preventing or arresting caries.

[Molecular detection and phylogenetic analysis of Wolbachia infection in common mosquito species in Henan Province]

OBJECTIVE

To investigate the infection and genotypes of Wolbachia in common mosquito species in Henan Province, so as to provide insights into management of mosquito-borne diseases.

METHODS

Aedes, Culex and Anopheles samples were collected from cowsheds, sheepfolds and human houses in Puyang, Nanyang City and Xuchang cities of Henan Province from July to September, 2022, and the infection of Wolbachia was detected. The 16S rDNA and wsp genes of Wolbachia were amplified and sequenced. Sequence alignment was performed using the BLAST software, and the obtained 16S rDNA gene sequence was compared with the sequence of the 16S rDNA gene in GenBank database. In addition, the phylogenetic trees were created based on 16S rDNA and wsp gene sequences using the software MEGA 11.0.

RESULTS

A total 506 female adult mosquitoes were collected from three sampling sites in Nanyang, Xuchang City and Puyang cities from July to September, 2022. The overall detection of Wolbachia was 45.1% (228/506) in mosquitoes, with a higher detection rate in A. albopictus than in Cx. pipiens pallens [97.9% (143/146) vs. 50.6% (85/168); χ2 = 88.064, P < 0.01]. The detection of Wolbachia in Cx. pipiens pallens was higher in Xuchang City (96.8%, 62/64) than in Nanyang (15.6%, 7/45) and Puyang cities (27.1%, 16/59) (χ2 = 89.950, P < 0.01). The homologies of obtained Wolbachia 16S rDNA and wsp gene sequences were 95.3% to 100.0% and 81.7% to 99.8%. Phylogenetic analysis based on wsp gene sequences showed Wolbachia supergroups A and B in mosquito samples, with wAlbA and wMors strains in supergroup A and wPip and wAlbB strains in supergroup B. Wolbachia strain wAlbB infection was detected in A. albopictus in Puyang and Nanyang Cities, while Wolbachia strain wPip infection was identified in A. albopictus in Xuchang City. Wolbachia strain wAlbA infection was detected in Cx. pipiens pallens sampled from three cities, and one Cx. pipiens pallens was found to be infected with Wolbachia strain wMors in Nanyang City.

CONCLUSIONS

Wolbachia infection is commonly prevalent in Ae. albopictus and Cx. pipiens pallens from Henan Province, and Wolbachia strains wAlbB and wAlbA are predominant in Ae. albopictus, while wPip strain is predominant in Cx. pipiens pallens. This is the first report to present Wolbachia wMors strain infection in Cx. pipiens pallens in Henan Province.

Distortion of Mendelian segregation across the Angus cattle genome uncovering regions affecting reproduction

Nowadays, the availability of genotyped trios (sire-dam-offspring) in the livestock industry enables the implementation of the transmission ratio distortion (TRD) approach to discover deleterious alleles in the genome. Various biological mechanisms at different stages of the reproductive cycle such as gametogenesis, embryo development and postnatal viability can induce signals of TRD (i.e., deviation from Mendelian inheritance expectations). In this study, TRD was evaluated using both SNP-by-SNP and sliding windows of 2-, 4-, 7-, 10- and 20-SNP across 92,942 autosomal SNPs for 258,140 genotyped Angus cattle including 7,486 sires, 72,688 dams and 205,966 offspring. Transmission ratio distortion was characterized using allelic (specific- and unspecific-parent TRD) and genotypic parameterizations (additive- and dominance-TRD). Across the Angus autosomal chromosomes, 851 regions were clearly found with decisive evidence for TRD. Among these findings, 19 haplotypes with recessive patterns (potential lethality for homozygote individuals) and 52 regions with allelic patterns exhibiting complete or quasi-complete absence for homozygous individuals in addition to under-representation (potentially reduced viability) of the carrier (heterozygous) offspring were found. In addition, 64 (12) and 20 (4) regions showed significant influence on the trait heifer pregnancy at p-value < 0.05 (after chromosome-wise false discovery rate) and 0.01, respectively, reducing the pregnancy rate up to 15%, thus, supporting the biological importance of TRD phenomenon in reproduction.

Transferability evaluation of the deep potential model for simulating water-graphene confined system

Machine learning potentials (MLPs) are poised to combine the accuracy of ab initio predictions with the computational efficiency of classical molecular dynamics (MD) simulation. While great progress has been made over the last two decades in developing MLPs, there is still much to be done to evaluate their model transferability and facilitate their development. In this work, we construct two deep potential (DP) models for liquid water near graphene surfaces, Model S and Model F, with the latter having more training data. A concurrent learning algorithm (DP-GEN) is adopted to explore the configurational space beyond the scope of conventional ab initio MD simulation. By examining the performance of Model S, we find that an accurate prediction of atomic force does not imply an accurate prediction of system energy. The deviation from the relative atomic force alone is insufficient to assess the accuracy of the DP models. Based on the performance of Model F, we propose that the relative magnitude of the model deviation and the corresponding root-mean-square error of the original test dataset, including energy and atomic force, can serve as an indicator for evaluating the accuracy of the model prediction for a given structure, which is particularly applicable for large systems where density functional theory calculations are infeasible. In addition to the prediction accuracy of the model described above, we also briefly discuss simulation stability and its relationship to the former. Both are important aspects in assessing the transferability of the MLP model.

Investigation of Polymer Aging Mechanisms Using Molecular Simulations: A Review

Aging has a serious impact on the properties of functional polymers. Therefore, it is necessary to study the aging mechanism to prolong the service and storage life of polymer-based devices and materials. Due to the limitations of traditional experimental methods, more and more studies have adopted molecular simulations to analyze the intrinsic mechanisms of aging. In this paper, recent advances in molecular simulations of the aging of polymers and their composites are reviewed. The characteristics and applications of commonly used simulation methods in the study of the aging mechanisms (traditional molecular dynamics simulation, quantum mechanics, and reactive molecular dynamics simulation) are outlined. The current simulation research progress of physical aging, aging under mechanical stress, thermal aging, hydrothermal aging, thermo-oxidative aging, electric aging, aging under high-energy particle impact, and radiation aging is introduced in detail. Finally, the current research status of the aging simulations of polymers and their composites is summarized, and the future development trend has been prospected.

Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes

Computational enzyme design has been successfully applied to identify new alternatives to natural enzymes for the biosynthesis of important compounds. However, the moderate catalytic activities of de novo designed enzymes indicate that the modeling accuracy of current computational enzyme design methods should be improved. Here, high-throughput molecular dynamics simulations were used to enhance computational enzyme design, thus allowing the identification of variants with higher activities in silico. Different time schemes of high-throughput molecular dynamics simulations were tested to identify the catalytic features of evolved Kemp eliminases. The 20 × 1 ns molecular dynamics simulation scheme was sufficiently accurate and computationally viable to screen the computationally designed massive variants of Kemp elimination enzymes. The developed hybrid computational strategy was used to redesign the most active Kemp eliminase, HG3.17, and five variants were generated and experimentally confirmed to afford higher catalytic efficiencies than that of HG3.17, with one double variant (D52Q/A53S) exhibiting a 55% increase. The hybrid computational enzyme design strategy is general and computationally economical, with which we anticipate the efficient creation of practical enzymes for industrial biocatalysis.

Computational design of quinone electrolytes for redox flow batteries using high-throughput machine learning and theoretical calculations

Molecular design of redox-active materials with higher solubility and greater redox potential windows is instrumental in enhancing the performance of redox flow batteries Here we propose a computational procedure for a systematic evaluation of organic redox-active species by combining machine learning, quantum-mechanical, and classical density functional theory calculations. 1,517 small quinone molecules were generated from the building blocks of benzoquinone, naphthoquinone, and anthraquinone with different substituent groups. The physics-based methods were used to predict HOMO-LUMO gaps and solvation free energies that account for the redox potential differences and aqueous solubility, respectively. The high-throughput calculations were augmented with the quantitative structure-property relationship analyses and machine learning/graph network modeling to evaluate the materials’ overall behavior. The computational procedure was able to reproduce high-performance cathode electrolyte materials consistent with experimental observations and identify new electrolytes for RFBs by screening 100,000 di-substituted quinone molecules, the largest library of redox-active quinone molecules ever investigated. The efficient computational platform may facilitate a better understanding of the structure-function relationship of quinone molecules and advance the design and application of all-organic active materials for RFBs.

Molecular Dynamics Simulation of Protein Cages

Molecular dynamics (MD) simulations enable the description of the physical movement of the system over time based on classical mechanics at various scales depending on the models. Protein cages are a particular group of different-size proteins with hollow, spherical structures and are widely found in nature, which have vast applications in numerous fields. The MD simulation of cage proteins is particularly important as a powerful tool to unveil their structures and dynamics for various properties, assembly behavior, and molecular transport mechanisms. Here, we describe how to conduct MD simulations for cage proteins, especially technical details, and analyze some of the properties of interest using GROMACS/NAMD packages.

Dietary Total Antioxidant Capacity and Cognitive Function in Older Adults in the United States: The NHANES 2011-2014

OBJECTIVES

Oxidative stress level takes part in the development of cognitive decline. However, the association between total antioxidant capacity (TAC) from diet and cognitive function is controversial. The aim of this study was to investigate the relationship between TAC and the cognitive function of older adults in the U.S.

DESIGN

A cross-sectional study.

SETTING

National Health and Nutrition Examination Surveys database.

PARTICIPANTS

2712 older adults aged over 60 years.

MEASUREMENTS

TAC was calculated from 8 antioxidative vitamins based on the reference values for vitamin C equivalent antioxidant capacity obtained from individuals' 24 h dietary recall. Four memory-related assessments were employed [Immediate Recall test (IRT), Delayed Recall test (DRT), Animal Fluency test (AFT), and Digit Symbol Substitution test (DSST)].

RESULTS

Among the 2712 participants, the median age was 68 years, and 50.4% were women. Participants in the group with higher TAC levels had relatively higher IRT, AFT and DSST scores (P=0.025, P=0.008, P<0.001, respectively). In adjusted weighted linear regression, log-transformed TAC was positively associated with AFT (β=1.10, 95%CI: 0.51, 1.70) and DSST (β=2.81, 95%CI: 1.16, 4.45). Compared with the first quartile, the participants in the second (Q2 vs. Q1, OR=0.66, 95%CI: 0.43,1.02) and fourth quartile (Q4 vs. Q1, OR=0.47, 95%CI:0.28, 0.78) of log-transformed TAC showed a decreased risk of impaired cognitive function (ICF) after adjusting for confounders. The dose-response analysis indicated a gradual descent in the risk of ICF as TAC increases. Diabetes mellitus (DM) mediated part of the effect of TAC on ICF. The relationship between TAC and ICF was more pronounced in subjects with DM (Q4 vs Q1, OR=0.36, 95%CI:0.17, 0.74).

CONCLUSION

Our findings support that higher dietary antioxidant potential was related to a decreased risk of cognitive dysfunction, particularly in the subjects with DM who may have oxidative injury. DM was one of the factors mediating the effect of TAC on ICF.

Ab Initio Molecular Dynamics Simulation of Water Transport through Short Carbon Nanotubes

Water transport through short single-walled (6, 6) carbon nanotubes (CNTs) was investigated with ab initio molecular dynamics (AIMD) simulation at different temperatures. The water molecules under extreme confinement present a one-dimensional jagged pattern owing to hydrogen bonding, with the near-perfect alignment of the dipole orientations. CNTs ending with dangling bonds can promote water dissociation near the entrance and the occurrence of dipole flipping along the water wire at high temperatures, accompanied by the formation of D defects and L defects in the hydrogen-bond network. In contrast, dissociation of water molecules rarely takes place if the dangling bonds at the ends of the CNTs are terminated with H atoms. Angular jumps of water molecules are commonplace inside the narrow CNTs, implying a low-energy barrier for hydrogen-bond exchange among water molecules in narrow CNTs. The simulation results demonstrate the high activity of dangling bonds at the ends of short CNTs, accompanying passivation processes and their profound impact on water structure and transport, which is important for diverse technological applications.

Immune checkpoint inhibitor-associated new-onset primary adrenal insufficiency: a retrospective analysis using the FAERS

BACKGROUND

Our study aimed to investigate the prevalence and demographic characteristics of immune checkpoint inhibitor-associated primary adrenal insufficiency (ICI-PAI) and to explore the risk factors of its clinical outcome using data from the US FDA Adverse Event Reporting System (FAERS).

METHODS

This was a retrospective study. All cases of new-onset or newly diagnosed primary adrenal insufficiency associated with FDA-approved ICIs from 1 January 2007 to 31 December 2020 were identified and collected using FAERS. Data on age, sex category, body weight of the participating individuals, the reporting year and the prognosis of cases, and other accompanying endocrinopathies related to ICIs, were analysed.

RESULTS

The incidence of ICI-PAI was 1.03% (1180/114121). Of the 1180 cases of PAI, 46 were "confirmed PAI", and 1134 were "suspected PAI". Combination therapy with anti-CTLA-4 and anti-PD-1 was related to a higher risk of PAI compared with the anti-PD-1-only group (χ² = 92.88, p < 0.001). Male and elderly individuals showed a higher risk of ICI-PAI (male vs. female, 1.17% vs. 0.94%, χ² = 12.55, p < 0.001; age < 65 vs. ≥ 65, 1.20 vs. 1.41%, χ² = 6.89, p = 0.009). The co-occurrence rate of endocrinopathies other than PAI was 24.3%, which showed a higher trend in patients on nivolumab-ipilimumab treatment than in those on PD-1 inhibitors (χ² = 3.227, p = 0.072). Body weight was negatively associated with the risk of death in the study population [p = 0.033 for the regression model; B = - 0.017, OR 0.984, 95% CI (0.969-0.998), p = 0.029].

CONCLUSION

ICI-associated PAI is a rare but important irAE. Male and elderly patients have a higher risk of ICI-PAI. Awareness among clinicians is critical when patients with a lower body weight develop PAI, which indicates a higher risk of a poor clinical outcome.

Circadian nuclear receptor Rev-erbalpha is expressed by platelets and potentiates platelet activation and thrombus formation

Background

Adverse cardiovascular events have day/night patterns with peaks in the morning, potentially related to endogenous circadian clock control of platelet activation. Circadian nuclear receptor Rev-erbα is an essential and negative component of the circadian clock.

Purpose

We aim to investigate the expression profile and biological function of Rev-erbα in platelets.

Methods and results

Here we report the presence and functions of circadian nuclear receptor Rev-erbα in human and mouse platelets. Both human and mouse platelet Rev-erbα showed a circadian rhythm that positively correlated with platelet aggregation. Global Rev-erbα knockout and platelet-specific Rev-erbα knockout mice exhibited defective in hemostasis as assessed by prolonged tail-bleeding times. Rev-erbα deletion also reduced ferric chloride-induced carotid arterial occlusive thrombosis, prevented collagen/epinephrine-induced pulmonary thromboembolism, and protected against microvascular microthrombi obstruction and infarct expansion in an acute myocardial infarction model. In vitro thrombus formation assessed by CD41-labeled platelet fluorescence intensity was significantly reduced in Rev-erbα knockout mouse blood. Platelets from Rev-erbα knockout mice exhibited impaired agonist-induced aggregation responses, integrin αIIbβ3 activation and α-granule release. Consistently, pharmacological inhibition of Rev-erbα by specific antagonists decreased platelet activation markers in both mouse and human platelets. Mechanistically, mass spectrometry and co-immunoprecipitation analyses revealed that Rev-erbα potentiated platelet activation via oligophrenin-1-mediated RhoA/ERM (ezrin/radixin/moesin) pathway.

Conclusion

We provide the first evidence that circadian protein Rev-erbα is functionally expressed in platelets and potentiates platelet activation and thrombus formation. Rev-erbα may serve as a novel therapeutic target for managing thrombosis-based cardiovascular disease.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): This work was supported by grants from the National Science Fund for Distinguished Young Scholars (81625002), the National Natural Science Foundation of China (81930007).

[Study on mechanisms of Th17/Treg imbalance in patients with cystic echinococcosis based on miRNA expression profiles]

OBJECTIVE

To investigate the serum microRNA (miRNA) expression and examine the impact of miRNA expression profiles on T helper type 17 (Th17)/regulatory T cells (Treg) imbalance among patients with cystic echinococcosis, so as to provide insights into the illustration of the mechanisms underlying chronic Echinococcus granulosus infections, and long-term pathogenesis.

METHODS

Total RNA was extracted from the sera of cystic echinococcosis patients and healthy controls, and subjected to high-throughput sequencing with the Illumina sequencing platform. Known miRNAs were annotated and new miRNAs were predicted using the miRBase database and the miRDeep2 tool, and differentially expressed miRNAs were identified. The target genes of differentially expressed miRNAs were predicted using the software miRanda and TargetScan, and the intersection was selected for Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Among the differentially expressed miRNAs with the 20 highest fold changes, miRNAs that targeted genes relating to key transcription factors RORC and FOXP3 that determine the production of Th17 and Treg cells or their important regulatory pathways (PI3K-Akt and mTOR pathways) were matched.

RESULTS

A total of 53 differentially expressed miRNAs were screened in sera of cystic echinococcosis patients and healthy controls, including 47 up-regulated miRNAs and 6 down-regulated miRNAs. GO enrichment analysis showed that these differentially expressed miRNA were involved DNA transcription and translation, cell components, cell morphology, neurodevelopment and metabolic decomposition, and KEGG pathway analysis showed that the differentially expressed miRNA were mainly involved in MAPK, PI3K-Akt and mTOR signaling pathways. Among the differentially expressed miRNAs with the 20 highest fold changes, there were 3 miRNAs that had a potential for target regulation of RORC, and 15 miRNAs that had a potential to target the PI3K-Akt and mTOR signaling pathways.

CONCLUSIONS

Significant changes are found in serum miRNA expression profiles among patients with E. granulosus infections, and differentially expressed miRNAs may lead to Th17/Treg imbalance through targeting the key transcription factors of Th17/Treg or PI3K-Akt and mTOR pathways, which facilitates the long-term parasitism of E. granulosus in hosts and causes a chronic disease.

First live birth in China after cryopreserved ovarian tissue transplantation to prevent premature ovarian insufficiency

OBJECTIVE

This article reports the first live birth after cryopreserved ovarian tissue transplantation to prevent premature ovarian insufficiency in China.

METHODS

A patient with myelodysplastic syndrome received ovarian tissue cryopreservation before hematopoietic stem cell transplantation, and six ovarian cortex strips were thawed and transplanted into her peritoneal pocket 2 years later.

RESULTS

Pregnancy occurred spontaneously 27 months after grafting, and a healthy girl was born at 38 weeks gestation. Until now, the child has developed normally without any major diseases.

CONCLUSIONS

We report the first live birth resulting from ovarian tissue cryopreservation and transplantation in China.

Heavy metal uptake by bryophytes and vascular plants in a manganese carbonate slag field, China

Slag produced in mining and smelting of manganese carbonate ore potentially pollutes the environment and endangers the health of humans and other living organisms. This study investigates the uptake of six heavy metals, Cu, Pb, Mn, Zn, Cr and Cd, by bryophytes and vascular plants growing on manganese carbonate slag in the Houshangou Slag Field near Zunyi City, Guizhou Province, China. Determination of heavy metal uptake in bryophytes and vascular plants may identify species suitable as biomonitors for bioremediation of polluted lands. Eight bryophyte taxa were identified in the study area; among which, Bryum argenteum and Physcomitrium eurystomum were dominant; life forms of bryophytes were predominantly short turfs. Three monocotyledons, all Poaceae, and five dicotyledons were recorded in four families. The highest heavy metal uptake in bryophytes, Mn content by B. argenteum, was more than 25,000 mg·kg^-1 . Furthermore, determination of heavy metal content in roots, leaves and fruits of six vascular plants demonstrated that each had a unique capacity for heavy metal accumulation: roots, leaves and fruits of similar plant species exhibited varying uptake capacity. Mn content in leaves was recorded in the order: B. davidii > A. tricolor > E. crus-galli > C. argentea > P. acinosa > C. album. In summary, B. argenteum, Echinochloa crus-galli and Phytolacca acinosa have strong enrichment capacity for heavy metals. These species could be used for comprehensive treatment of heavy metal pollution in electrolytic Mn slag fields, and for bioremediation of polluted areas associated with Mn mining and processing.

Importance of the Subunit-Subunit Interface in Ferritin Disassembly: A Molecular Dynamics Study

Ferritin is a spherical cage-like protein that is useful for loading large functional particles for various applications. To our knowledge, how pH affects the interfaces inside ferritin and the mechanism of ferritin disassembly is far from complete. For this article, we conducted a series of molecular dynamics simulations (MD) at different pH values to study how interfaces affect ferritins' stability. It is shown that dimers are stable even at extremely low pH (pH 2.0), indicating that the dimer is the essential subunit for disassembly, and the slight swelling of the dimer resulting from monomer rotation inside a dimer is what triggers disassembly. During ferritin disassembly, there are two types of interfaces involved, and the interface between dimers is crucial. We also found that the driving forces for maintaining dimer stability are different when a dimer is inside ferritin and in an acidic solution. At low pH, the protonation of residues can lead to the loss of the salt bridge and the hydrogen bond between dimers, resulting in the disassembly of ferritin in an acidic environment. The above simulations reveal the possible mechanism of ferritin disassembly in an acidic solution, which can help us to design innovative and functional ferritin cages for different applications.

The role of conformational dynamics on the activity of polymer-conjugated CalB in organic solvents

A perennial interest in enzyme catalysis has been expanding its applicability from aqueous phase where enzymes are naturally evolved to organic solvents in which the majority of industrial chemical synthesis...

[Intestinal flora polymorphisms with different lesional stages in an animal model of MAFLD]

Objective: To study the intestinal flora specific differences with different lesional stages of metabolic (disorder) associated fatty liver disease (MAFLD), namely simple steatosis and steatohepatitis, so as to provide a new direction for MAFLD-related intestinal flora transplantation and targeted therapy. Methods: Mice were fed with normal diet, methionine-choline deficient diet (MCD) and a high-fat high-fructose diet (HFHF) for 12 weeks to construct simple steatosis and steatohepatitis models. HE and Sirius scarlet staining was performed to observe the liver pathological changes. The qPCR method was used to evaluate inflammation and liver fibrosis factors. A fully automatic biochemical analyzer was used to detect changes in liver transaminase and blood lipids. 16S rRNA sequencing method was used to observe the intestinal flora differences in the feces of each group of mice. The comparison of means between two groups was performed by t-test, and the comparison of means between multiple groups was performed by one-way analysis of variance. Kruskal-Wallis rank sum test was used for non-normally distributed data. Results: NAFLD scores were determined with pathological sections (HE and Sirius scarlet staining) of mice liver, which showed that the inflammation and liver fibrosis scores of the MCD and HFHF groups were 2.12 ± 0.18 and 1.06 ± 0.24, and 2.22 ± 0.16 and 0.46 ± 0.10, respectively. The degree of liver inflammation and fibrosis was significantly higher in the MCD than the HFHF group (P < 0.001 and P < 0.01). Lipid deposition was higher in the HFHF than the MCD group (P < 0.001), and the scores were 2.36 ± 0.17 and 1.60 ± 0.24 respectively. Simultaneously, the inflammatory [tumor necrosis factor-A (TNF-a), chemokine factor-2 (CXCL-2)] and hepatic fibrosis indicators [vascular smooth muscle actin alpha (a-SMA) and connective tissue growth factor (CTGF)] had confirmed the above-mentioned results at the transcription level. Moreover, the intestinal flora diversity was reduced (P < 0.05) in the MCD group than the HFHF group, and the Simpson and Shannon index were 0.31 ± 0.10 and 0.42 ± 0.05, and 2.03 ± 0.33 and 1.70 ± 0.28, respectively, and the differences were significant between different intestinal flora groups. The levels of Desulfovibrio, Odoribacter, and Roseburia flora were significantly increased in the HFHF than the MCD group, and the levels of Faecalibaculum, Parasutterella, Alipis, Butyricimonas_virosa, Turicibacter_sp, and Romboutsia_ilealis were significantly increased in the MCD than the HFHF group, and the difference was statistically significant (P < 0.05). Conclusion: There are significant differences in intestinal flora diversity between simple steatosis and steatohepatitis models. Therefore, clarifying the difference between the two may provide a new direction for the stage manner treatment of MAFLD.

A distal regulatory strategy of enzymes: from local to global conformational dynamics

Modulating the distribution of various states in protein ensembles through distal sites may be promising in the evolution of enzymes in desired directions. However, the prediction of distal mutation hotspots that stabilize the favoured states from a computational perspective remains challenging. Here, we presented a strategy based on molecular dynamics (MD) and Markov state models (MSM) to predict distal mutation sites. Extensive MD combined with MSM was applied to determine the principally distributed metastable states interconverting at a slow timescale. Then, molecular docking was used to classify these states into active states and inactive ones. Distal mutation hotspots were targeted based on comparing the conformational features between active and inactive states, where mutations destabilize the inactive states and show little influence on the active state. The proposed strategy was used to explore the highly dynamic MHETase, which shows a potential application in the biodegradation of poly(ethylene terephthalate) (PET). Seven principally populated interrelated metastable states were identified, and the atomistic picture of their conformational changes was unveiled. Several residues at distal positions were found to adopt more H-bond occupancies in inactive states than active states, making them potential mutation hotspots for stabilizing the favoured conformations. In addition, the detailed mechanism revealed the significance of calcium ions at a distance from the catalytic centre in reshaping the free energy landscape. This study deepens the understanding of the conformational dynamics of α/β hydrolases containing a lid domain and advances the study of enzymatic plastic degradation.

Plasma metabolomics in perioperative period of defect repair in patients with pulmonary arterial hypertension associated with congenital heart disease

Background

The pathophysiological alterations in response to shunt correction in patients with pulmonary arterial hypertension associated with congenital heart disease (CHD-PAH) is still not clear.

Purpose

To explore the dynamic plasma metabolite profiling and its relationship with clinical characteristics in patients with CHD-PAH during the perioperative period of defect repair.

Methods

Plasma samples from 13 patients with CHD-PAH were harvested at four time points: before cardiopulmonary bypass (CPB) after anesthesia (Pre), immediately after CPB (T0), 24 h (T24), and 48 h (T48) after defect repair. The untargeted metabolomics strategy based on UPLC Q-TOF MS was used to detect the metabolites. Clinical measures were recorded at indicated time points.

Results

The sample distribution at four time points was well separated (Figure 1A, B). 193 metabolites were distinguished at different time points according to Variable Important in Projection (VIP) score (Figure 1C), enriched in pathways such as carnitine synthesis, phospholipid biosynthesis and oxidation of branched chain fatty acids (Figure 2A). 17 metabolites alterations were significantly correlated with gradients in mean pulmonary arterial pressure (mPAP) at T48 versus Pre, indicative of the response to defect correction (Figure 2B). Intriguingly, 4 out of the 17 (23.5%) metabolites including propionylcarnitine, butenylcarnitine, isobutyryl-L-carnitine and hexanoylcarnitine were enriched in oxidation of branched chain fatty acids. They were increased at both T24 and T48 (all P&lt;0.05 except propionylcarnitine with P&lt;0.05 at T24) (Figure 2C).

Conclusions

This is the first study to show the altered metabolic profiles of CHD-PAH patients in perioperative period of defect repair. Metabolites that respond to shunt correction could be a suitable non-invasive marker and would be of great value in disease monitoring and evaluating future therapeutic interventions.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): 13th Five-Year Plan–Precise Medicine–Key Research and Development Program–Clinical Cohort of Rare Disease; National Natural Science Foundation of China Figure 1. Overall analysis of metabolitesFigure 2. Shunt correction associated metabolites

The synergistic mechanisms of apo-ferritin structural transitions and Au(iii) ion transportation: molecular dynamics simulations with the Markov state model

Due to its unique structure, recent years have witnessed the use of apo-ferritin to accumulate various non-natural metal ions as a scaffold for nanomaterial synthesis. However, the transport mechanism of metal ions into the cavity of apo-ferritin is still unclear, limiting the rational design and controllable preparation of nanomaterials. Here, we conducted all-atom classical molecular dynamics (MD) simulations combined with Markov state models (MSMs) to explore the transportation behavior of Au(iii) ions. We exhibited the complete transportation paths of Au(iii) from solution into the apo-ferritin cage at the atomic level. We also revealed that the transportation of Au(iii) ions is accompanied by coupled protein structural changes. It is shown that the 3-fold axis channel serves as the only entrance with the longest residence time of Au(iii) ions. Besides, there are eight binding clusters and five 3-fold structural metastable states, which are important during Au(iii) transportation. The conformational changes of His118, Asp127, and Glu130, acting as doors, were observed to highly correlate with the Au(iii) ion's position. The MSM analysis and Potential Mean Force (PMF) calculation suggest a remarkable energy barrier near Glu130, making it the rate-limiting step of the whole process. The dominant transportation pathway is from cluster 3 in the 3-fold channel to the inner cavity to cluster 5 on the inner surface, and then to cluster 6. These findings provide inspiration and theoretical guidance for the further rational design and preparation of new nanomaterials using apo-ferritin.

First pregnancy in China after ovarian tissue transplantation to prevent premature ovarian insufficiency

OBJECTIVE

This article reports the first case of pregnancy after frozen-thawed ovarian tissue transplantation to prevent iatrogenic premature ovarian insufficiency in China.

METHODS

Ovarian tissue cryopreservation was performed in a patient with myelodysplastic syndrome (MDS) before multi-agent chemotherapy and hematopoietic stem cell transplantation. Two years later, she showed complete remission from MDS, and six frozen-thawed ovarian tissue strips were transplanted into the peritoneal pocket.

RESULTS

The patient's ovarian activity was restored 3 months after transplantation, and pregnancy occurred spontaneously 27 months after grafting. Until now, the pregnancy has progressed for 30 weeks, and the repeated ultrasound showed normal fetal development.

CONCLUSION

This is the first pregnancy resulting from ovarian tissue cryopreservation and transplantation in China.

Prenatal exposure to solar radiation and hypertensive disorders of pregnancy

OBJECTIVE

To examine the association between prenatal exposure to solar radiation and hypertensive disorders of pregnancy (HDP).

DESIGN

A multicentre retrospective study.

SETTING

19 hospitals in the USA.

POPULATION

205 888 women with singleton gestation from the Consortium on Safe Labor (2002-2008).

MAIN OUTCOME MEASURES

Gestational hypertension, pre-eclampsia/eclampsia, and pre-eclampsia superimposed on chronic hypertension.

METHODS

Medical records of the participants were linked to solar radiation obtained from the National Solar Radiation Database. Average daily solar radiation of each woman was estimated over the entire pregnancy period and over three trimesters during pregnancy according to hospital sites. Generalised estimated equation was applied to investigate the relationship between quartiles of average daily solar radiation and HDP. Restricted cubic spline was applied to assess the nonlinear associations.

RESULTS

Higher average solar radiation during the entire pregnancy was associated with reduced risks of HDP. Compared with the 1st quartile of solar radiation during the entire pregnancy, odds ratios (ORs) of the 2nd, 3rd and 4th quartiles were respectively 0.80 (95% CI 0.72-0.90), 0.63 (95% CI 0.55-0.73), 0.65 (95% CI 0.54-0.78) for gestational hypertension; 0.66 (95% CI 0.57-0.76), 0.61 (95% CI 0.51-0.73), 0.77 (95% CI 0.62-0.95) for pre-eclampsia, and 0.44 (95% CI 0.36-0.55), 0.42 (95% CI 0.35-0.49), 0.60 (95% CI 0.46-0.78) for superimposed pre-eclampsia.

CONCLUSION

Exposure to higher daily solar radiation during pregnancy is associated with a decreased risk of HDP. The protective effect was stronger for superimposed pre-eclampsia than for pre-eclampsia or gestational hypertension.

TWEETABLE ABSTRACT

Exposure to higher daily solar radiation during pregnancy is associated with a decreased risk of HDP.

[Immune regulatory effect of tacrolimus in patients with severe aplastic anemia and in murine model]

Objective: To investigate the immunomodulatory effect of tacrolimus in severe aplastic anemia (SAA). Methods: Patients diagnosed with SAA at the Department of Hematology, General Hospital of Tianjin Medical University from June 2015 to January 2018 were enrolled. CD8⁺T cells were sorted by immunomagnetic separation from peripheral blood of SAA patients. MTT method was used to detect the proliferation of CD8⁺T cells. The SAA mouse model was established by total body irradiation (TBI) and donor lymphocyte infusion (DLI). There were 10 normal controls without pretreatment, 10 rats in TBI group, 15 rats received TBI and DLI. The expression of perforin and granzyme in CD8⁺T cells and the ratio of CD4⁺/CD8⁺cells in peripheral circulation were measured by flow cytometry. The level of interferon-γ (IFN-γ) in medium supernatant of cultured CD8⁺T cells was tested with enzyme-linked immunosorbent assay (ELISA). SAA mouse model was established to study the recovery of hemogram and survival time after treatment. Results: A total of 16 SAA patients were enrolled, and there were 10 males and 6 females, with a median age of 35 (22-49) years. Tacrolimus inhibited the proliferation of CD8⁺T cells when IL-2 concentration was 20.0,200.0 and 2 000.0 U/ml (P<0.05). The expression of perforin in CD8⁺T cells of SAA patients treated with tacrolimus was significantly lower than that in blank control group and IL-2 group [(2.25±0.76)%, (6.70±0.82)% vs (9.10±1.90)%,all P<0.05]. The level of IFN-γ in CD8⁺T cells group after applying tacrolimus was significantly lower than that in the blank control group (P<0.05). After 10 days of administration, the peripheral blood hemoglobin (Hb), white blood cell (WBC) and platelet (PLT) counts of SAA mice in tacrolimus group were all higher than those in SAA group (all P<0.05). The expression of perforin in CD8⁺T cells in tacrolimus group was significantly lower than that in SAA group [(18. 39±6.65) vs (29. 99±9.83),P<0.05]. The median survival time of SAA group was 18.6 days, and the 90 day survival rate was 0. The median survival time of tacrolimus group was 44.6 days, and the 90 day survival rate was 80%. The survival time of SAA mice in tacrolimus group was significantly longer than that in SAA group (P<0.05). Conclusion: The immunomodulatory effect of tacrolimus in SAA is similar to CsA. It has an immunosupressive effect on CD8⁺T lymphocyte.