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.

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.

An Antidehydration Hydrogel Based on Zwitterionic Oligomers for Bioelectronic Interfacing.

Hydrogels are ideal interfacing materials for on-skin healthcare devices, yet their susceptibility to dehydration hinders their practical use. While incorporating hygroscopic metal salts can prevent dehydration and maintain ionic conductivity, concerns arise regarding metal toxicity due to the passage of small ions through the skin barrier. Herein, an antidehydration hydrogel enabled by the incorporation of zwitterionic oligomers into its network is reported. This hydrogel exhibits exceptional water retention properties, maintaining ≈88% of its weight at 40% relative humidity, 25 °C for 50 days and about 84% after being heated at 50 °C for 3 h. Crucially, the molecular weight design of the embedded oligomers prevents their penetration into the epidermis, as evidenced by experimental and molecular simulation results. The hydrogel allows stable signal acquisition in electrophysiological monitoring of humans and plants under low-humidity conditions. This research provides a promising strategy for the development of epidermis-safe and biocompatible antidehydration hydrogel interfaces for on-skin devices.

Mitochondrial nucleoid condensates drive peripheral fission through high membrane curvature.

Mitochondria are dynamic organelles that undergo fusion and fission events, in which the mitochondrial membrane and DNA (mtDNA) play critical roles. The spatiotemporal organization of mtDNA reflects and impacts mitochondrial dynamics. Herein, to study the detailed dynamics of mitochondrial membrane and mtDNA, we rationally develop a dual-color fluorescent probe, mtGLP, that could be used for simultaneously monitoring mitochondrial membrane and mtDNA dynamics via separate color outputs. By combining mtGLP with structured illumination microscopy to monitor mitochondrial dynamics, we discover the formation of nucleoid condensates in damaged mitochondria. We further reveal that nucleoid condensates promoted the peripheral fission of damaged mitochondria via asymmetric segregation. Through simulations, we find that the peripheral fission events occurred when the nucleoid condensates interacted with the highly curved membrane regions at the two ends of the mitochondria. Overall, we show that mitochondrial nucleoid condensates utilize peripheral fission to maintain mitochondrial homeostasis.

Enhancing Prosthetic Control through High-Fidelity Myoelectric Mapping with Molecular Anchoring Technology.

Myoelectric control utilizes electrical signals generated from the voluntary contraction of remaining muscles in an amputee's stump to operate a prosthesis. Precise and agile control requires low-level myoelectric signals (below 10% of maximum voluntary contraction, MVC) from weak muscle contractions such as phantom finger or wrist movements, but imbalanced calcium concentration in atrophic skin can distort the signals. This is due to poor ionic-electronic coupling between skin and electrode, which often causes excessive muscle contraction, fatigue, and discomfort during delicate tasks. To overcome this challenge, a new strategy called molecular anchoring is developed to drive hydrophobic molecular effectively interact with and embed into stratum corneum for high coupling regions between ionic fluxes and electronic currents. The use of hydrophobic poly(N-vinyl caprolactam) gel has resulted in an interface impedance of 20 kΩ, which is 1/100 of a commercial acrylic-based electrode, allowing the detection of ultralow myoelectric signals (≈1.5% MVC) that approach human limits. With this molecular anchoring technology, amputees operate a prosthesis with greater dexterity, as phantom finger and wrist movements are predicted with 97.6% accuracy. This strategy provides the potential for a comfortable human-machine interface when amputees accomplish day-to-day tasks through precise and dexterous myoelectric control.

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.

Double-Transmembrane Domain of SNAREs Decelerates the Fusion by Increasing the Protein-Lipid Mismatch.

SNARE is the essential mediator of membrane fusion that highly relies on the molecular structure of SNAREs. For instance, the protein syntaxin-1 involved in neuronal SNAREs, has a single transmembrane domain (sTMD) leading to fast fusion, while the syntaxin 17 has a V-shape double TMDs (dTMDs), taking part in the autophagosome maturation. However, it is not clear how the TMD structure influences the fusion process. Here, we demonstrate that the dTMDs significantly reduce fusion rate compared with the sTMD by using an in vitro reconstitution system. Through theoretical analysis, we reveal that the V-shape dTMDs can significantly increase protein-lipid mismatch, thereby raising the energy barrier of the fusion, and that increasing the number of SNAREs can reduce the energy barrier or protein-lipid mismatch. This study provides a physicochemical mechanistic understanding of SNARE-regulated membrane fusion.

2D MoS2 and BN Nanosheets Damage Mitochondria through Membrane Penetration.

With the progression of nanotechnology, a growing number of nanomaterials have been created and incorporated into organisms and ecosystems, which raises significant concern about potential hazards of these materials on human health, wildlife, and the environment. Two-dimensional (2D) nanomaterials are one type of nanomaterials with thicknesses ranging from that of a single atom or of several atoms and have been proposed for a variety of biomedical applications such as drug delivery and gene therapy, but the toxicity thereof on subcellular organelles remains to be studied. In this work, we studied the impact of two typical 2D nanomaterials, MoS2 and BN nanosheets, on mitochondria, which are a type of membranous subcellular organelle that provides energy to cells. While 2D nanomaterials at a low dose exhibited a negligible cell mortality rate, significant mitochondrial fragmentation and partially reduced mitochondrial functions occurred; cells initiate mitophagy in response to mitochondrial damages, which cleans damaged mitochondria to avoid damage accumulation. Moreover, the molecular dynamics simulation results revealed that both MoS2 and BN nanosheets can spontaneously penetrate the mitochondrial lipid membrane through the hydrophobic interaction. The membrane penetration induced heterogeneous lipid packing resulting in damages. Our results demonstrate that even at a low dose 2D nanomaterials can physically damage mitochondria by penetrating the membrane, which draws attention to carefully evaluating the cytotoxicity of 2D nanomaterials for the potential biomedical application.

Quantifying Shear-induced Margination and Adhesion of Platelets in Microvascular Blood Flow.

Platelet margination and adhesion are two critical and closely related steps in thrombus formation. Using dissipative particle dynamics (DPD) method that seamlessly models blood cells, blood plasma, and vessel walls with functionalized surfaces, we quantify the shear-induced margination and adhesion of platelets in microvascular blood flow. The results show that the occurrence of shear-induced RBC-platelet collisions has a remarkable influence on the degree of platelet margination. We characterize the lateral motion of individual platelets by a mean square displacement analysis of platelet trajectories, and find that the wall-induced lift force and the shear-induced displacement in wall-bounded flow cause the variation in near-wall platelet distribution. We then investigate the platelet adhesive dynamics under different flow conditions, by conducting DPD simulations of blood flow in a microtube with fibrinogen-coated wall surfaces. We find that the platelet adhesion is enhanced with the increase of fibrinogen concentration level but decreased with the increase of shear rate. These results are consistent with available experimental results. In addition, we demonstrate that the adherent platelets have a negative impact on the margination dynamics of the circulating platelets, which is mainly due to the climbing effect induced by the adherent ones. Taken together, these findings provide useful insights into the platelet margination and adhesion dynamics, which may facilitate the understanding of the predominant processes governing the initial stage of thrombus formation.

Inhibition of Amyloid Nucleation by Steric Hindrance.

Despite recent experiments and simulations suggesting that small-molecule inhibitors and some post-translational modifications (e.g., glycosylation and ubiquitination) can suppress the pathogenic aggregation of proteins due to steric hindrance, the effect of steric hindrance on amyloid formation has not been systematically studied. Based on Monte Carlo simulations using a coarse-grained model for amyloidogenic proteins and a hard sphere acting as steric hindrance, we investigated how steric hindrance on proteins could affect amyloid formation, particularly two steps of primary nucleation, namely, oligomerization and conformational conversion into a ß-sheet-enriched nucleus. We found that steric spheres played an inhibitory role in oligomerization with the effect proportional to the sphere radius RS, which we attributed to the decline in the nonspecific attractions between proteins. During the second step, small steric spheres facilitated the conformational conversion of proteins while large ones suppressed the conversion. The overall steric effect on amyloid nucleation was inhibitory regardless of RS. As RS increased, oligomeric assemblies changed from amorphous into sheet-like, structurally ordered species, reminiscent of the structure of amyloid fibrils. The oligomers with large RS were off-pathway with their ordered structures induced by the competition between steric hindrance and nonspecific attractions of soluble proteins. Interestingly, the equimolar mixture of proteins with and without steric hindrance amplified the sterically inhibitory effect by increasing the energy barrier of protein's conformational conversion. The physical mechanisms and biological implications of the above results are discussed. Our findings improve the current understanding of how nature regulates protein aggregation and amyloid formation by steric hindrance.

Self-Reporting Joule Heating Modulated Stiffness of Polymeric Nanocomposites for Shape Reconfiguration.

Shape reconfigurable devices, e.g., foldable phones, have emerged with the development of flexible electronics. But their rigid frames limit the feasible shapes for the devices. To achieve freely changeable shapes yet keep the rigidity of devices for user-friendly operations, stiffness-tunable materials are desired, especially under electrical control. However, current such systems are multilayer with at least a heater layer and a structural layer, leading to complex fabrication, high cost, and loss of reprocessability. Herein, we fabricate covalent adaptable networks-carbon nanotubes (CAN-CNT) composites to realize Joule heating controlled stiffness. The nanocomposites function as stiffness-tunable matrices, electric heaters, and softening sensors all by themselves. The self-reporting of softening is used to regulate the power control, and the sensing mechanism is investigated by simulating the CNT-polymer chain interactions at the nanoscale during the softening process. The nanocomposites not only have adjustable mechanical and thermodynamic properties but also are easy to fabricate at low cost and exhibit reprocessability and recyclability benefiting from the dynamic exchange reactions of CANs. Shape and stiffness control of flexible display systems are demonstrated with the nanocomposites as framing material, where freely reconfigurable shapes are realized to achieve convenient operation, wearing, or storage, fully exploiting their flexible potential.

Flunarizine suppresses Mycobacterium tuberculosis growth via calmodulin-dependent phagosome maturation.

Tuberculosis (TB), an infectious bacterial disease caused by Mycobacterium tuberculosis (Mtb), is a major cause of death worldwide. Multidrug-resistant TB remains a public health crisis and thus novel effective treatments, such as host-directed therapies (HDTs), are urgently required to overcome the challenges of TB infection. In this study, we evaluated 4 calcium modulators for their effects on Mtb growth in macrophages. Only flunarizine enhanced the bactericidal ability of macrophages against Mtb, which was induced by an increase in phosphorylated calcium/calmodulin (CaM)-dependent protein kinase II (pCaMKII) levels. We further discovered that the expression of CaM was decreased in Mtb-infected macrophages and restored following flunarizine treatment; this was associated with phagolysosome maturation and acidification. Consistent with these findings, the anti-TB ability of macrophages was reduced following the silencing of CaM or inhibition of CAMKII activity. In conclusion, our results demonstrated that flunarizine enhanced the bactericidal ability of macrophages and clarified its CaM-pCAMKII-dependent mechanism. Therefore, our findings strongly support further studies of this currently approved drug as an HDT candidate for TB therapy.

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.

Investigations on the dissolved organic matter leached from oil-contaminated soils by using pyrolysis remediation method.

Pyrolysis, as a convenient and fast technology, has been proved to be promising in the remediation of oil-contaminated soil. However, little is known about the dissolved organic matter (DOM) associated with pyrolyzed oil-contaminated soil and its environmental impact. Herein, optical spectroscopic techniques (i.e., absorbance and fluorescence) were adopted to reveal the relationship between the pyrolysis temperature and the characteristics of the DOM and the associated phytotoxicity. Results show that one of the main factors determining the properties and phytotoxicity of DOM leached from the pyrolyzed soil is the critical temperature (approximately 325 °C) during pyrolysis. When the temperature was lower than 325 °C, more types and quantities of DOM, mainly fulvic acid-like substances, were desorbed from the soil with the temperature, which have little effect on wheat growth. However, when the temperature was in the range of 325-550 °C, the type and quantity of DOM increased first and then decreased as the temperature increased, during which the organic matter in the soil decomposed. The wheat growth was first inhibited and then promoted. Finally, the correlation between the spectral indices of DOM with the phytotoxicity suggested that fluorescent components identified by parallel factor analysis were positively correlated with phytotoxicity. This study indicates the pyrolytic remediation of oil-contaminated soil should avoid some critical temperature ranges.

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.

A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection.

BACKGROUND: Real-time reverse transcription-PCR (rRT-PCR) has been the most effective and widely implemented diagnostic technology since the beginning of the COVID-19 pandemic. However, fuzzy rRT-PCR readouts with high Ct values are frequently encountered, resulting in uncertainty in diagnosis. METHODS: A Specific Enhancer for PCR-amplified Nucleic Acid (SENA) was developed based on the Cas12a trans-cleavage activity, which is specifically triggered by the rRT-PCR amplicons of the SARS-CoV-2 Orf1ab (O) and N fragments. SENA was first characterized to determine its sensitivity and specificity, using a systematic titration experiment with pure SARS-CoV-2 RNA standards, and was then verified in several hospitals, employing a couple of commercial rRT-PCR kits and testing various clinical specimens under different scenarios. FINDINGS: The ratio (10 min/5 min) of fluorescence change (FC) with mixed SENA reaction (mix-FCratio) was defined for quantitative analysis of target O and N genes, and the Limit of Detection (LoD) of mix-FCratio with 95% confidence interval was 1.2≤1.6≤2.1. Totally, 295 clinical specimens were analyzed, among which 21 uncertain rRT-PCR cases as well as 4 false negative and 2 false positive samples were characterized by SENA and further verified by next-generation sequencing (NGS). The cut-off values for mix-FCratio were determined as 1.145 for positive and 1.068 for negative. INTERPRETATION: SENA increases both the sensitivity and the specificity of rRT-PCR, solving the uncertainty problem in COVID-19 diagnosis and thus providing a simple and low-cost companion diagnosis for combating the pandemic. FUNDING: Detailed funding information is available at the end of the manuscript.

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.