NLRP12 Senses the SARS-CoV-2 Membrane Protein and Promotes an Inflammatory Response.

COVID-19 is an acute respiratory disorder that is caused by SARS-CoV-2, in which excessive systemic inflammation is associated with adverse patient clinical outcomes. Here, we observed elevated expression levels of NLRP12 (nucleotide-binding leucine-rich repeat-containing receptor 12) in human peripheral monocytes and lung tissue during infection with SARS-CoV-2. Co-immunoprecipitation analysis revealed that NLRP12 directly interacted with the M protein through its leucine-rich repeat domain. Moreover, in vitro studies demonstrated that NLRP12 interacted with TRAF3 and promoted its ubiquitination and degradation, which counteracted the inhibitory effect of TRAF3 on the NF-κB/MAPK signaling pathway and promoted the production of inflammatory cytokines. Furthermore, an in vivo study revealed that NLRP12 knockout mice displayed attenuated tissue injury and ameliorated inflammatory responses in the lungs when infected with a SARS-CoV-2 M protein-reconstituted pseudovirus and mouse coronavirus. Taken together, these findings suggest that NLRP12 mediates the inflammatory responses during coronavirus infection.

Binding kinetics study of SARS-CoV-2 main protease and potential inhibitors via molecular dynamics simulations.

The pandemic COVID-19 was induced by the novel coronavirus SARS-CoV-2. The virus main protease (Mpro) cleaves the coronavirus polyprotein translated from the viral RNA in the host cells. Because of its crucial role in virus replication, Mpro is a potential drug target for COVID-19 treatment. Herein, we study the interactions between Mpro and three HIV-1 protease (HIV-1 PR) inhibitors, Lopinavir (LPV), Saquinavir (SQV), Ritonavir (RIT), and an inhibitor PF-07321332, by conventional and replica exchange molecular dynamics (MD) simulations. The association/dissociation rates and the affinities of the inhibitors were estimated. The three HIV-1 PR inhibitors exhibit low affinities, while PF-07321332 has the highest affinity among these four simulated inhibitors. Based on cluster analysis, the HIV-1 PR inhibitors bind to Mpro at multiple sites, while PF-07321332 specifically binds to the catalytically activated site of Mpro. The stable and specific binding is because PF-07321332 forms multiple H-bonds to His163 and Glu166 simultaneously. The simulations suggested PF-07321332 could serve as an effective inhibitor with high affinity and shed light on the strategy of drug design and drug repositioning.

Cellular mechanics of wound formation in single cell layer under cyclic stretching.

Wounds can be produced when cells and tissues are subjected to excessive forces, for instance, under pathological conditions or nonphysiological loading. However, the cellular behaviors in the wound formation process are not clear. Here we tested the behaviors of wound formation in the epithelial layer with an in-suit uniaxial stretching device. We found that the wound often nucleates at the position where the cells are dividing. The polarization direction of cells near the wound is preferentially along the wound edge, whereas the cells far from the wound are preferentially perpendicular to the stretching direction. The larger the wound area is, the higher is the aspect ratio of the cells around the wound. Increasing the cell density will strengthen the cell layer. The higher the cell density is, the smaller is the area of the wounds, and the weaker is the effect of stretching on the polarization of the cells. Furthermore, we built a coarse-grained cell model that can explicitly consider the elasticity and viscoelasticity of cells, cell-cell interaction, and cell active stress, by which we simulated the wound formation process and quantitatively analyzed the force and stress fields in the cell layer, particularly around the wound. These analyses reveal the cellular mechanisms of wound formation behaviors in the cell layer under stretching and shed useful light on tissue engineering and regenerative medicine for biomedical applications.

One-tube SARS-CoV-2 detection platform based on RT-RPA and CRISPR/Cas12a.

BACKGROUND: COVID-19 has spread rapidly around the world, affecting a large percentage of the population. When lifting certain mandatory measures for an economic restart, robust surveillance must be established and implemented, with nucleic acid detection for SARS-CoV-2 as an essential component. METHODS: We tried to develop a one-tube detection platform based on RT-RPA (Reverse Transcription and Recombinase Polymerase Isothermal Amplification) and DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR) technology, termed OR-DETECTR, to detect SARS-CoV-2. We designed RT-RPA primers of the RdRp and N genes following the SARS-CoV-2 gene sequence. We optimized reaction components so that the detection process could be carried out in one tube. Specificity was demonstrated by detecting nucleic acid samples from pseudoviruses from seven human coronaviruses and Influenza A (H1N1). Clinical samples were used to validate the platform and all results were compared to rRT-PCR. RNA standards and pseudoviruses diluted by different gradients were used to demonstrate the detection limit. Additionally, we have developed a lateral flow assay based on OR-DETECTR for detecting COVID-19. RESULTS: The OR-DETECTR detection process can be completed in one tube, which takes approximately 50 min. This method can specifically detect SARS-CoV-2 from seven human coronaviruses and Influenza A (H1N1), with a low detection limit of 2.5 copies/µl input (RNA standard) and 1 copy/µl input (pseudovirus). Results of six samples from SARS-CoV-2 patients, eight samples from patients with fever but no SARS-CoV-2 infection, and one mixed sample from 40 negative controls showed that OR-DETECTR is 100% consistent with rRT-PCR. The lateral flow assay based on OR-DETECTR can be used for the detection of COVID-19, and the detection limit is 2.5 copies/µl input. CONCLUSIONS: The OR-DETECTR platform for the detection of COVID-19 is rapid, accurate, tube closed, easy-to-operate, and free of large instruments.

Membrane packing defects in synaptic vesicles recruit complexin and synuclein.

Complexin-1 (Cpx) and α-synuclein (α-Syn) are involved in neurotransmitter release through an interaction with synaptic vesicles (SVs). Recent studies demonstrated that Cpx and α-Syn preferentially associate with highly curved membranes, like SVs, to correctly position them for fusion. Here, based on recent experimental results, to further propose a possible explanation for this mechanism, we performed in silico simulations probing interactions between Cpx or α-Syn and membranes of varying curvature. We found that the preferential association is attributed to smaller, curved membranes containing more packing defects that expose hydrophobic acyl tails, which may favorably interact with hydrophobic residues of Cpx and α-Syn. The number of membrane defects is proportional to the curvature and the size can be regulated by cholesterol.

How Does Nature Evade the "Larger is Weaker" Fate of Ultralong Silk ß-Sheet Nanocrystallites.

Silk protein builds up one of the strongest fibers superior to most synthetic and natural polymers. However, the strengthening mechanisms of the silk proteins remain largely elusive because of their complex nanocomposite structures. Here, we report an unusual behavior of this kind of material that is distinctively different from those of metals and other polymers. We find that there are multiple interface microcracks nucleating and stacking under the shear loading, dividing the interchain interface into small segments, by which the silk protein can achieve a high strength even with the ultralong chains. This is a new strategy of microstructure design of soft matter that could avoid the "larger is weaker" fate due to the increase of the chain length. This novel mechanism is crucial for building strong polymer materials with long chain molecules and at the same time retaining their complex functional and structural properties.

O-GlcNAcylation inhibits the oligomerization of alpha-synuclein by declining intermolecular hydrogen bonds through a steric effect.

Toxic abnormal aggregation of α-synuclein (α-Syn) is a feature of Parkinson's disease. Several biochemical and biophysical studies have demonstrated that many post-translational modifications (PTM) of α-Syn could distinctly alleviate its oligomerization-mediated toxicity. Recently, a compelling link is emerging between the PTM O-GlcNAcylation (O-GlcNAc) and protein aggregation, yet the underlying molecular mechanism remains unclear. Based on the all-atom molecular dynamics simulations, we found that O-GlcNAc modifications can suppress the process of oligomerization of α-Syn aggregates via a steric effect-the additional O-linked glycosyl group disrupts the formation of hydrogen bonds (H-bonds) between α-Syn monomers. Besides, we proposed a theoretical model to further capture the physical mechanism of α-Syn aggregation/disaggregation in the absence/presence of O-GlcNAc-modified α-Syn. Our findings unveil the molecular mechanism of the O-GlcNAc-induced inhibition of α-Syn oligomerization, which may help to understand how O-GlcNAc prevents the oligomerization of other proteins and provides the guideline for the development of O-GlcNAc-based therapeutic strategies in neurodegenerative diseases.

Bidirectional regulation of configuration of the carbon nanotube containing a water droplet.

Carbon nanotube complexes are known for their miraculous mechanical and electronic properties that are crucial for nano-electromechanical systems (MEMS). In this study, through molecular dynamics simulations we found for the first time that the electric field and temperature can be used to co-regulate a reversible change of cross-sectional configuration of single-wall carbon nanotubes (SWCNTs). We showed that the electric field can help induce the collapse of an SWCNT when it contains a water droplet, while the increase of temperature can quickly recover its configuration. This controllable bistability of SWCNTs is promising for the design of nanodevices such as electromechanical switches in NEMS.

Intravoxel Incoherent Motion Combined With Dynamic Contrast-Enhanced Perfusion MRI of Early Cervical Carcinoma: Correlations Between Multimodal Parameters and HIF-1α Expression.

BACKGROUND: The identification of hypoxia inducible factor (HIF-1α) expression is helpful for the quantitative assessment of tumor hypoxia. The application of multimodal imaging techniques may play a part in the assessment of HIF-1α expression of cervical carcinoma. PURPOSE: To investigate the correlations between multiple imaging parameters and HIF-1α expression of early cervical carcinoma and to determine whether tumor hypoxia can be predicted using multisequence imaging parameters. STUDY TYPE: Prospective observational. POPULATION: One hundred patients with early cervical carcinoma. FIELD STRENGTH/SEQUENCES: 3.0 T MRI including intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) and dynamic contrast-enhanced (DCE) perfusion MRI sequences. ASSESSMENT: DCE-MRI and IVIM DWI were performed for all patients. The imaging parameters included volume transfer constant (Ktrans ), rate constant (Kep ), extravascular extracellular volume fraction (Ve ), D, D*, and f. STATISTICAL TESTS: The comparisons of imaging parameters between two independent groups were performed using the Mann-Whitney U-test. Multiple linear regression analysis was performed to determine the correlation between multiple imaging parameters and HIF-1α expression. The diagnostic ability of DCE-MRI, IVIM DWI, and the combination of two techniques for discriminating high-expression and low-expression groups were analyzed. RESULTS: The high-expression group had a lower Ktrans or Kep value than the low-expression group (P = 0.03; 0.02), while the high-expression group had a higher Ve value than the low-expression group (P = 0.03). The high-expression group had a higher D or f value than the low-expression group (P = 0.02; 0.02). Ktrans , Kep , D, Ve , and f values were independently correlated with HIF-1α expression. The sensitivity or accuracy of a combined method was higher than that of DCE-MRI or IVIM DWI individually (P = 0.03, 0.02; 0.04, 0.03). DATA CONCLUSION: The combination of DCE-MRI and IVIM DWI can improve the diagnostic ability of discriminating different HIF-1α expression levels for early cervical tumors. LEVEL OF EVIDENCE: 1 Technical Efficacy Stage: 2 J. Magn. Reson. Imaging 2019;50:918-929.

Highly stable and selective measurement of Fe3+ ions under environmentally relevant conditions via an excitation-based multiwavelength method using N, S-doped carbon dots.

Fast and accurate detection of Fe3+ under relevant natural conditions is important in environmental monitoring. In this study, an improved and simplified fluorescence method based on the multiwavelength luminescence in the visible region and the avoidance of the self-quenching property of N, S-doped carbon dots (NSC-Dots) was developed for the first time to determine Fe3+ concentration under varied environmental conditions. This method can simultaneously save time and provide accurate information. The as-prepared NSC-Dots exhibit two stable excitation peaks from 200 nm to 450 nm at a fixed emission wavelength (λem = 450 nm). A standard equation (R2 = 0.995) can be derived by measuring the quenching degree of the two peaks and referring to Stern-Volmer theory. Thus, Fe3+ concentration was accurately determined. The interference of the environmentally relevant concentrations of other metal ions, humic acid, and pH on Fe3+ measurement was tested. Results showed that the standard equation can be used to accurately determine Fe3+ concentration within the range of the 95% prediction band. The fast and facile multiwavelength method may facilitate the real-time monitoring of Fe3+ concentration in complex water environments.

Intravoxel incoherent motion MR imaging of early cervical carcinoma: correlation between imaging parameters and tumor-stroma ratio.

OBJECTIVES: To investigate if intravoxel incoherent motion (IVIM) MR imaging can predict the tumour-stroma ratio (TSR) in patients with early cervical carcinoma. METHODS: Fifty-four patients with early cervical carcinoma were prospectively enrolled into this study. All patients underwent IVIM imaging and parameters including D, D* and f value were measured. The tumours were classified into stroma-rich and stroma-poor group according to TSR, and comparisons of IVIM parameters between two groups were performed. The relationships between IVIM parameters and TSR were analysed by using a multivariate multi-regression analysis. RESULTS: D and f values were significantly lower in stroma-poor tumours than in stroma-rich tumours (p=0.02, 0.04), while the difference in D* value between two groups didn't achieve statistical significance (p=0.09). The areas under ROC curves of D and f values in discriminating stroma-rich and stroma-poor tumours were 0.835 (95%CI=0.616~0.905) and 0.686 (95%CI=0.575~0.798). In multiple linear regression analysis, D value, pathologic type, histologic grade, tumour size and f value were independently correlated with TSR of cervical carcinoma. CONCLUSIONS: D and f values are independently correlated with TSR of cervical carcinoma and have the potential for quantitative measurement of TSR. KEY POINTS: • TSR is a recognized independent prognostic factor in many solid tumours. • D and f values measured by IVIM MRI are independently correlated with TSR while D* is not. • IVIM offers the potential to predict TSR.

Cholesterol suppresses membrane leakage by decreasing water penetrability.

Membrane fusion is a fundamental biological process that lies at the heart of enveloped virus infection, synaptic signaling, intracellular vesicle trafficking, gamete fertilization, and cell-cell fusion. Membrane fusion is initiated as two apposed membranes merge to a single bilayer called a hemifusion diaphragm. It is believed that the contents of the two fusing membranes are released through a fusion pore formed at the hemifusion diaphragm, and yet another possible pathway has been proposed in which an undefined pore may form outside the hemifusion diaphragm at the apposed membranes, leading to the so-called leaky fusion. Here, we performed all-atom molecular dynamics simulations to study the evolution of the hemifusion diaphragm structure with various lipid compositions. We found that the lipid cholesterol decreased water penetrability to inhibit leakage pore formation. Biochemical leakage experiments support these simulation results. This study may shed light on the underlying mechanism of the evolution pathways of the hemifusion structure, especially the understanding of content leakage during membrane fusion.

Remediation of Petroleum-Contaminated Soil and Simultaneous Recovery of Oil by Fast Pyrolysis.

Petroleum-contaminated soil (PCS) caused by the accidental release of crude oil into the environment, which occurs frequently during oil exploitation worldwide, needs efficient and cost-effective remediation. In this study, a fast pyrolysis technology was implemented to remediate the PCS and concurrently recover the oil. The remediation effect related to pyrolytic parameters, the recovery rate of oil and its possible formation pathway, and the physicochemical properties of the remediated PCS and its suitability for planting were systematically investigated. The results show that 50.9% carbon was recovered in oil, whose quality even exceeds that of crude oil. Both extractable total petroleum hydrocarbon (TPH) and water-soluble organic matter (SOM) in PCS were completely removed at 500 °C within 30 min. The remaining carbon in remediated PCS was determined to be in a stable and innocuous state, which has no adverse effect on wheat growth. On the basis of the systematically characterizations of initial PCS and pyrolytic products, a possible thermochemical mechanism was proposed which involves evaporation, cracking and polymerization. In addition, the energy consumption analysis and remediation effect of various PCSs indicate that fast pyrolysis is a viable and cost-effective method for PCS remediation.

The effects of environmental conditions on the enrichment of antibiotics on microplastics in simulated natural water column.

Concerns regarding the release of microplastics (MPs) into the environment led us to explore the relationship between the different environmental factors and physicochemical properties of MPs, as well as the change of interaction between MPs and organic pollutants. In this study, the effects of environmental factors (ageing conditions), such as pH, temperature, ionic strength, ageing time, and humic acid (HA) concentration, on the characteristics of MPs and their adsorption toward tetracycline (TC) were systematically investigated. The results showed that ageing factors such as pH, ionic strength, and temperature were found to have little impact on the adsorptive capacity of MPs for TC. However, MPs aged in HA solution exhibited a significant decreased adsorptive capacity for TC. HA, which has numerous functional groups, can cover the surface of MPs and change their hydrophobicity, thereby reducing the adsorption affinity to TC. The electrostatic repulsion between adsorbed HA and TC molecules may also decrease the adsorption of TC. In addition, the competing effect of HA for adsorption sites on the surface of MPs further reduces the adsorption of TC. The data presented in this work provide useful information for understanding the transfer of antibiotics by aged MPs, which is of fundamental importance to assess the environmental impact of MPs.

Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case.

Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems.

Lipid molecules influence early stages of yeast SNARE-mediated membrane fusion.

Lipid molecules, structural components of biomembranes, have been proposed for an important role in membrane fusion. Through various techniques based on a protein-reconstituted vesicle-vesicle fusion system, we investigated the influence of several lipid molecules on different stages of a yeast soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-mediated membrane fusion process. Lipid compositions played a significant role in the early stages, docking and lipid mixing, while only exhibiting a minor effect on fusion pore formation and dilation phases, indicated by both small and large content mixing.

Predicted rupture force of a single molecular bond becomes rate independent at ultralow loading rates.

We present for the first time a theoretical model of studying the saturation of the rupture force of a single molecular bond that causes the rupture force to be rate independent under an ultralow loading rate. This saturation will obviously bring challenges to understanding the rupture behavior of the molecular bond using conventional methods. This intriguing feature implies that the molecular bond has a nonzero strength at a vanishing loading rate. We find that the saturation behavior is caused by bond rebinding when the loading rate is lower than a limiting value depending on the loading stiffness.

Thermochemical behavior of tris(2-butoxyethyl) phosphate (TBEP) during co-pyrolysis with biomass.

Co-pyrolysis of plastic waste and wood biomass to recover valuable chemicals is a cost-effective waste-recycling technology. However, widely used organophosphate ester additives in plastic, such as tris(2-butoxyethyl) phosphate (TBEP), can form diverse phosphorus (P)-containing species. These P-containing compounds can pose new environmental challenges when the biochar is reused. In this study, a mixture of TBEP and lignin was used to simulate the feedstock of plastic waste and wood biomass, and the thermochemical behavior of TBEP in slow pyrolysis (20 K min(-1)) and fast pyrolysis at 400-600 °C was investigated. The results show that low temperature in fast pyrolysis favors the enrichment of P in char. Up to 76.6% of initial P in the feedstock is retained in the char resulting from 400 °C, while only 51% is retained in the char from 600 °C. Slow pyrolysis favors the formation of stable P species regardless of the temperature; only 7% of the P retained in the char is extractable from char from slow pyrolysis, while 20-40% of P can be extracted from char resulting from fast pyrolysis. The addition of CaCl2 and MgCl2 can significantly increase the fraction of P retained in the char by the formation of Ca, Mg-P compounds. Online TG-FTIR-MS analysis suggests that TBEP undergoes decomposition through different temperature-dependent pathways. The P-containing radicals react with the aromatic rings produced by the pyrolysis of lignin to form Ar-P species, which is an important factor influencing the distribution and stabilization of P in char.

[Retrospective analysis of the efficacy and safety of anti-hepatitis B virus drugs taken during pregnancy in women from the Guangdong Province].

OBJECTIVE: To investigate the efficacy of anti-hepatitis B virus (HBV) drugs for preventing vertical transmission of HBV and the safety of these drugs when given as treatment during pregnancy (to women) or insemination (to men). METHODS: Cases of women and men who had taken anti-HBV drug therapy during pregnancy or insemination, respectively, were retrospectively selected for study from among 18 hospitals and 33 specialists in the Guangdong Province. Demographic, HBV infection and treatment data was collected for puerperal men or women and their newborns from the medical records. RESULTS: A total of 122 cases with detailed follow-up data were included in the study and including 74 women who were administered lamivudine (LAM) more than telbivudine (LdT) more than adefovir (ADV)more than entecavir (ETV) (hierarchy ranking by number of cases) and 48 men who were administered LAM more than ADV more than LdT more than ETV.None of the 122 newborns related to these cases showed HBV infection at 7 months of follow-up.None of the 74 puerperal women showed complications related to reproduction.There was one ease of a newborn being underweight at birth (2.1 kg), for which the mother had taken LdT during pregnancy. There was also one case of a newborn with a harelip and one case of a newborn with an inguinal hernia, for which both of the fathers had taken ADV during the time of insemination. CONCLUSION: This retrospective investigation carried out in Guangdong Province indicated that not only are anti-HBV drugs efficacious for blocking vertical transmission of HBV but also are safe for both mothers and infants when taken by fathers or mothers during the reproduction phases of insemination and pregnancy.

Frustrated Lewis pair catalyst realizes efficient green diesel production.

Hydrotreating renewable oils over sulfided metal catalysts is commercially applied to produce green diesel, but it requires a continuous sulfur replenishment to maintain catalyst activity, which inevitably results in sulfur contamination and increases production costs. We report a robust P-doped NiAl-oxide catalyst with frustrated Lewis pairs (i.e., P atom bonded with the O atom acts as an electron donor, while the spatially separated Ni atom acts as an electron acceptor) that allows efficient green diesel production without sulfur replenishment. The catalyst runs more than 500 h at a weight hourly space velocity (WHSV) of 28.3 h-1 without deactivation (methyl laurate as a model compound), and is able to completely convert a real feedstock of soybean oil to diesel-range hydrocarbons with selectivity >90% during 500 h of operation. This work is expected to open up a new avenue for designing non-sulfur catalysts that can make the green diesel production greener.