Pulsed rise and growth of the Tibetan Plateau to its northern margin since ca. 30 Ma.

The onset of mountain building along margins of the Tibetan Plateau provides a key constraint on the processes by which the high topography in Eurasia formed. Although progressive expansion of thickened crust underpins most models, several studies suggest that the northern extent of the plateau was established early, soon after the collision between India and Eurasia at ca. 50 Ma. This inference relies heavily on the age and provenance of Cenozoic sediments preserved in the Qaidam basin. Here, we present evidence in the northern plateau for a considerably younger inception and evolution of the Qaidam basin, based on magnetostratigraphies combined with detrital apatite fission-track ages that date the basin fills to be from ca. 30 to 4.8 Ma. Detrital zircon-provenance analyses coupled with paleocurrents reveal that two-stage growth of the Qilian Shan in the northeastern margin of the Tibetan Plateau began at ca. 30 and at 10 Ma, respectively. Evidence for ca. 30 and 10 to 15 Ma widespread synchronous deformation throughout the Tibetan Plateau and its margins suggests that these two stages of outward growth may have resulted from the removal of mantle lithosphere beneath different portions of the Tibetan Plateau.

Recent Advances in Understanding of the Singlet Oxygen in Energy Storage and Conversion.

Singlet oxygen (term symbol 1 Δg , hereafter 1 O2 ), a reactive oxygen species, has recently attracted increasing interest in the field of rechargeable batteries and electrocatalysis and photocatalysis. These sustainable energy conversion and storage technologies are of vital significance to replace fossil fuels and promote carbon neutrality and finally tackle the energy crisis and climate change. Herein, the recent progresses of 1 O2 for energy storage and conversion is summarized, including physical and chemical properties, formation mechanisms, detection technologies, side reactions in rechargeable batteries and corresponding inhibition strategies, and applications in electrocatalysis and photocatalysis. The formation mechanisms and inhibition strategies of 1 O2 in particular aprotic lithium-oxygen (Li-O2 ) batteries are highlighted, and the applications of 1 O2 in photocatalysis and electrocatalysis is also emphasized. Moreover, the confronting challenges and promising directions of 1 O2 in energy conversion and storage systems are discussed.

Development of IL-17A inhibitor-induced atopic dermatitis-like rash in psoriasis patients: Insights into immune shift.

Cases of atopic dermatitis (AD)-like rash induced by IL-17A inhibitor secukinumab treatment (SI-AD) have been recently reported in psoriasis patients. To identify immune and inflammatory factors expression in SI-AD. A panel of 15 immune and inflammatory factors in peripheral blood samples from various groups, including patients with patients with SI-AD, psoriasis with secukinumab (S-stable), advanced psoriasis patients (Advanced) and healthy controls (HC). Interleukin-10 (IL-10), IL-4 and IL-17A were detected in skin tissue biopsy samples by immunohistochemistry and real-time quantitative polymerase chain reaction. The immunoglobulin E levels in the SI-AD patients exceeded normal values. The IL-10 levels in SI-AD patients were higher than those in S-stable patients, advanced patients and HC. The IL-4 levels in SI-AD patients were higher than that in S-stable patients and HC. The IL-17A levels in SI-AD patients were higher than those in advanced psoriasis patients and HC, but no significant differences were observed between SI-AD patients and S-stable patients. IL-10 and IL-4 levels were higher in AD-like rashes than in healthy skin, while IL-17A did not differ significantly between the two. Upon discontinuing secukinumab, and switching to oral cyclosporine, antihistamines, Janus kinase 1 inhibitor and topical glucocorticoids, SI-AD patients experienced significant improvement in their skin lesions. Upon reexamination, all 15 immune and inflammatory factors returned to normal levels. Immune shift from Th17 towards Th2 may occur in SI-AD, as indicated by abnormal expression of multiple immune and inflammatory factors observed in peripheral blood and skin tissues.

A Highly Stable Microporous Calcium-Based MOF for C2H2/CO2 Separation with Low Regenerative Energy.

Most of the porous materials used for acetylene/carbon dioxide separation have the problems of poor stability and high energy requirements for regeneration, which significantly hinder their practical application in industries. Here, we report a novel calcium-based metal-organic framework (NKM-123) with excellent chemical stability against water, acids, and bases. Additionally, it has exceptional thermal stability, retaining its structural integrity at temperatures up to 300 °C. This material exhibits promising potential for separating C2H2 and CO2 gases. Furthermore, it demonstrates an adsorption heat of 29.3 kJ mol-1 for C2H2, which is lower than that observed in the majority of MOFs used for C2H2/CO2 separations. The preferential adsorption of C2H2 over that of CO2 is confirmed by dispersion-corrected density functional theory (DFT-D) calculations. In addition, the potential of industrial feasibility of NKM-123 for C2H2/CO2 separation is confirmed by transient breakthrough tests. The robust cycle performance and structural stability of NKM-123 during multiple breakthrough tests show great potential in the industrial separation of light hydrocarbons.

Cross-subunit interactions that stabilize open states mediate gating in NMDA receptors.

NMDA receptors are excitatory channels with critical functions in the physiology of central synapses. Their activation reaction proceeds as a series of kinetically distinguishable, reversible steps, whose structural bases are currently under investigation. Very likely, the earliest steps include glutamate binding to glycine-bound receptors and subsequent constriction of the ligand-binding domain. Later, three short linkers transduce this movement to open the gate by mechanical pulling on transmembrane helices. Here, we used molecular and kinetic simulations and double-mutant cycle analyses to show that a direct chemical interaction between GluN1-I642 (on M3 helix) and GluN2A-L550 (on L1-M1 linker) stabilizes receptors after they have opened and thus represents one of the structural changes that occur late in the activation reaction. This native interaction extends the current decay, and its absence causes deficits in charge transfer by GluN1-I642L, a pathogenic human variant.

Proximity ligation initiated DNAzyme-powered catalytic hairpin assembly for sensitive and accurate microRNA analysis.

MicroRNAs (miRNAs) play a significant role in regulating diverse physiological processes, and are regarded as novel diagnostic biomarkers. However, the sensitive and reliable miRNA detection remains a huge challenge. Herein, we propose a proximity ligated initiated magnesium ion (Mg2+)-dependent DNAzyme-powered signal cascade for sensitive, accurate and reliable detection of miRNAs. Three signal amplification processes are involved in this approach, including the target miRNA recycle, DNAzyme powered substrate cleavage, and catalytic hairpin reaction (CHA). Based on this, the approach shows a low limit of detection of 523 aM and a wide detection range of 7 orders of magnitudes, which is comparable or superior to most of the former miRNA detection methods. In addition, the approach also possesses a high selectivity to target miRNA, suggesting a potential promising future of the approach for rapid detection of miRNAs in the application of developing novel tools for skin cancer diagnosis, and recovery evaluation.

Complex functional phenotypes of NMDA receptor disease variants.

NMDA receptors have essential roles in the physiology of central excitatory synapses and their dysfunction causes severe neuropsychiatric symptoms. Recently, a series of genetic variants have been identified in patients, however, functional information about these variants is sparse and their role in pathogenesis insufficiently known. Here we investigate the mechanism by which two GluN2A variants may be pathogenic. We use molecular dynamics simulation and single-molecule electrophysiology to examine the contribution of GluN2A subunit-residues, P552 and F652, and their pathogenic substitutions, P552R and F652V, affect receptor functions. We found that P552 and F652 interact during the receptors' normal activity cycle; the interaction stabilizes receptors in open conformations and is required for a normal electrical response. Engineering shorter side-chains at these positions (P552A and/or F652V) caused a loss of interaction energy and produced receptors with severe gating, conductance, and permeability deficits. In contrast, the P552R side chain resulted in stronger interaction and produced a distinct, yet still drastically abnormal electrical response. These results identify the dynamic contact between P552 and F652 as a critical step in the NMDA receptor activation, and show that both increased and reduced communication through this interaction cause dysfunction. Results show that subtle differences in NMDA receptor primary structure can generate complex phenotypic alterations whose binary classification is too simplistic to serve as a therapeutic guide.

Predicting allosteric sites using fast conformational sampling as guided by coarse-grained normal modes.

To computationally identify cryptic binding sites for allosteric modulators, we have developed a fast and simple conformational sampling scheme guided by coarse-grained normal modes solved from the elastic network models followed by atomistic backbone and sidechain reconstruction. Despite the complexity of conformational changes associated with ligand binding, we previously showed that simply sampling along each of the lowest 30 modes can adequately restructure cryptic sites so they are detectable by pocket finding programs like Concavity. Here, we applied this method to study four classical examples of allosteric regulation (GluR2 receptor, GroEL chaperonin, GPCR, and myosin). Our method along with alternative methods has been utilized to locate known allosteric sites and predict new promising allosteric sites. Compared with other sampling methods based on extensive molecular dynamics simulation, our method is both faster (1-2 h for an average-size protein of ∼400 residues) and more flexible (it can be easily integrated with any structure-based pocket finding methods), so it is suitable for high-throughput screening of large datasets of protein structures at the genome scale.

Facile synthesis of spherical covalent organic frameworks for enrichment and quantification of aryl organophosphate esters in mouse serum and tissues.

Here, an imine-linked-based spherical covalent organic framework (COF) was prepared at room temperature. The as-synthesized spherical COF served as an adsorbent in dispersive solid-phase extraction (dSPE), by its virtue of great surface area (1542.68 m2 /g), regular distribution of pore size (2.95 nm), and excellent stability. Therefore, a simple and high-efficiency dispersive solid phase extraction method based on a spherical COF coupled with high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was established to determine aryl organophosphate esters in biological samples. This approach displayed favorable linearity in the range of 10.0-1000.0 ng/L (r > 0.9989), a high signal enhancement factor (58.8-181.8 folds) with low limits of detection (0.3-3.3 ng/L). Moreover, it could effectively eliminate complex matrix interference to accurately extract seven aryl organophosphate esters from mouse serum and tissue samples with spiked recoveries of 82.0%-117.4%. The as-synthesized spherical COF has been successfully applied in sample preparation. The dSPE-HPLC-MS/MS method based on a spherical COF has potential application to study the pollutants' metabolism in vivo.

EIF3H knockdown inhibits malignant melanoma through regulating cell proliferation, apoptosis and cell cycle.

Malignant melanoma (MM) causes 80% of skin cancer-related deaths and becomes the most lethal type of skin cancer. The molecular mechanism of MM is still not clear. This study aimed to reveal the relationship between MM and EIF3H. Clinical specimens were collected to preliminarily explore the role of EIF3H in MM. MM cell lines with EIF3H knockdown were constructed for investigating the effects of EIF3H on cell proliferation, apoptosis, cell cycle and cell motility. Mice xenograft model was constructed for verification in vivo. We found that EIF3H was obviously upregulated in MM tissues compared with normal skin tissues, which was correlated with tumor stage and risk of lymphatic metastasis. The in vitro results indicated that silencing EIF3H in MM cells could significantly suppress cell proliferation, promote cell apoptosis and induce cell cycle arrest. Moreover, EIF3H knockdown significantly restrained cell motility through regulating EMT-related proteins. The effects of EIF3H knockdown were also verified in mice xenograft model, which were represented by slower growth rate, smaller volume and lighter weight of tumors. Therefore, EIF3H was identified as a critical factor in the development and progression of MM which may be used as a novel therapeutic target in the treatment of MM.

Predicting cryptic ligand binding sites based on normal modes guided conformational sampling.

To greatly expand the druggable genome, fast and accurate predictions of cryptic sites for small molecules binding in target proteins are in high demand. In this study, we have developed a fast and simple conformational sampling scheme guided by normal modes solved from the coarse-grained elastic models followed by atomistic backbone refinement and side-chain repacking. Despite the observations of complex and diverse conformational changes associated with ligand binding, we found that simply sampling along each of the lowest 30 modes is near optimal for adequately restructuring cryptic sites so they can be detected by existing pocket finding programs like fpocket and concavity. We further trained machine-learning protocols to optimize the combination of the sampling-enhanced pocket scores with other dynamic and conservation scores, which only slightly improved the performance. As assessed based on a training set of 84 known cryptic sites and a test set of 14 proteins, our method achieved high accuracy of prediction (with area under the receiver operating characteristic curve >0.8) comparable to the CryptoSite server. Compared with CryptoSite and other methods based on extensive molecular dynamics simulation, our method is much faster (1-2 hours for an average-size protein) and simpler (using only pocket scores), so it is suitable for high-throughput processing of large datasets of protein structures at the genome scale.

Predicting lipid and ligand binding sites in TRPV1 channel by molecular dynamics simulation and machine learning.

As a key cellular sensor, the TRPV1 channel undergoes a gating transition from a closed state to an open state in response to many physical and chemical stimuli. This transition is regulated by small-molecule ligands including lipids and various agonists/antagonists, but the underlying molecular mechanisms remain obscure. Thanks to recent revolution in cryo-electron microscopy, a growing list of new structures of TRPV1 and other TRPV channels have been solved in complex with various ligands including lipids. Toward elucidating how ligand binding correlates with TRPV1 gating, we have performed extensive molecular dynamics simulations (with cumulative time of 20 µs), starting from high-resolution structures of TRPV1 in both the closed and open states. By comparing between the open and closed state ensembles, we have identified state-dependent binding sites for small-molecule ligands in general and lipids in particular. We further use machine learning to predict top ligand-binding sites as important features to classify the closed vs open states. The predicted binding sites are thoroughly validated by matching homologous sites in all structures of TRPV channels bound to lipids and other ligands, and with previous functional/mutational studies of ligand binding in TRPV1. Taken together, this study has integrated rich structural, dynamic, and functional data to inform future design of small-molecular drugs targeting TRPV1.

Perillaldehyde Alleviates Spinal Cord Ischemia-Reperfusion Injury Via Activating the Nrf2 Pathway.

BACKGROUND: Spinal Cord ischemia-reperfusion injury (SCII) is one of the most destructive complications in thoracic-abdominal aortic surgery, which can cause physical abnormalities, paralysis and even brain death. Evidence has shown that perillaldehyde (PAH) can ameliorate rat's cerebra ischemia-reperfusion injury. However, the effect of PAH on SCII remains unknown. METHODS: The current study established SCII rat models and oxygen and glucose deprivation/reoxygenation-induced BV2 microglia models to explore whether PAH could alleviate SCII symptoms and to investigate underlying mechanism. RESULTS: SCII rats underwent severe neurologic motor dysfunction and histopathologic injury compared with the normal rats, which are exhibited by loss of motor neurons and decrease of nissl bodies. Treatment with PAH significantly ameliorated motor dysfunction and neuron damage. PAH downregulated the expression of NLR family pyrin domain containing 3, cleaved/pro caspase-1, interleukin-1ß and interleukin-18 in spinal cord tissues of SCII rats. Besides, the contents of oxidative stress-related factors superoxide dismutase, manganese-dependent superoxide dismutase, catalase and glutathione peroxidase were significantly increased and malondialdehyde content was decreased after PAH treatment. PAH treatment upregulated the expression of nuclear factor-E2-related factor 2 and heme oxygenase-1 in spinal cord tissues of SCII rats. Our in vitro study confirmed that PAH inhibited microglial activation by activating the nuclear factor-E2-related factor 2/heme oxygenase-1 pathway, exhibited by alleviated inflammation and oxidative stress. CONCLUSIONS: This study elucidates that PAH has the potential value for treating SCII, which provides an experimental basis for clinical trials in the future.

Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation.

The ryanodine receptors (RyR) are essential to calcium signaling in striated muscles. A deep understanding of the complex Ca2+ -activation/inhibition mechanism of RyRs requires detailed structural and dynamic information for RyRs in different functional states (eg, with Ca2+ bound to activating or inhibitory sites). Recently, high-resolution structures of the RyR isoform 1 (RyR1) were solved by cryo-electron microscopy, revealing the location of a Ca2+ binding site for activation. Toward elucidating the Ca2+ -modulation mechanism of RyR1, we performed extensive molecular dynamics simulation of the core RyR1 structure in the presence and absence of activating and solvent Ca2+ (total simulation time is >5 µs). In the presence of solvent Ca2+ , Ca2+ binding to the activating site enhanced dynamics of RyR1 with higher inter-subunit flexibility, asymmetric inter-subunit motions, outward domain motions and partial pore dilation, which may prime RyR1 for subsequent channel opening. In contrast, the solvent Ca2+ alone reduced dynamics of RyR1 and led to inward domain motions and pore contraction, which may cause inhibition. Combining our simulation with the map of disease mutation sites in RyR1, we constructed a wiring diagram of key domains coupled via specific hydrogen bonds involving the mutation sites, some of which were modulated by Ca2+ binding. The structural and dynamic information gained from this study will inform future mutational and functional studies of RyR1 activation and inhibition by Ca2+ .

Analysis of the Borehole Effect in Borehole Radar Detection.

The directional borehole radar can accurately locate and image the geological target around the borehole, which overcomes the shortcomings that the conventional borehole radar can only detect the depth of the target and the distance from the borehole. The directional borehole radar under consideration consists of a transmitting antenna and four receiving antennas equally distributed on the ring in the borehole. The nonuniformity caused by the borehole and sonde, as well as the mutual coupling among the four receiving antennas, will have a serious impact on the received signal and then cause interference to the azimuth recognition for the targets. In this paper, Finite difference time domain (FDTD), including the subgrid, is applied to study these effects and interferences, and the influence of borehole, sonde, and mutual coupling among the receiving antennas is found. The results show that, without considering the sonde and the fluid in the borehole, the one transmitting and one receiving borehole radar system does not have resonance, but the wave pattern of the reflected wave will have obvious distortion. For the four receiving antennas of the borehole radar system, there is obvious resonance, which is caused by the multiple reflections between the receiving antennas. However, when the fluid in the borehole is water and the relative permittivity of the sonde is low to a certain extent, the resonance disappears; that is, the generation of resonance requires a large relative permittivity material between the receiving antennas. When the influence of the sonde is considered, the resonance disappears because the relative permittivity of the sonde is low, which makes the propagation speed of the electromagnetic wave between the antennas accelerate and lose the conditions for resonance. In addition, the diameters of the sonde and the circular array of the receiving antennas can affect the received signal: the higher the diameter of the sonde and the higher the diameter of the circular array are, the better the differentiation of the received signal. The development of the research provides scientific guidance for the design and application of borehole radar in the future.

[Advances in quality research of Cinnamomum cassia].

Cinnamomum cassis is one of the commonly used traditional Chinese medicines in China. Its genuine producing areas distribute in Guangdong and Guangxi provinces. As an important edible herb and export variety of China, the quality control and internationalization of quality standards of C. cassis is extremely significant. In the recent years, with the development of the cinnamon industry, relevant academic research and the upgrade of the international standards, it is necessary to summarize the quality-related progress of C. cassis. In the present review, the germplasm resources, specific quality marker(Q-marker) and quality standards of C. cassis were summarized on the basis of published research during the last 10 years.

Molecular dynamics simulation of tropomyosin bound to actins/myosin in the closed and open states.

Tropomyosin (Tpm) is a dimeric coiled-coil protein that binds to filamentous actin, and regulates actin-myosin interaction by moving between three positions corresponding to the blocked, closed, and open states. To elucidate how Tpm undergoes transitions between these functional states, we have built structural models and conducted extensive molecular dynamics simulations of the Tpm-actins/myosin complex in the closed and open states (total simulation time >1.4 µs). Based on the simulation trajectories, we have analyzed the dynamics and energetics of a truncated Tpm interacting with actins/myosin under the physiological conditions. Our simulations have shown distinct dynamics of four Tpm periods (P3-P6), featuring pronounced biased fluctuations of P4 and P5 toward the open position in the closed state, which is consistent with a conformational selection mechanism for Tpm-regulated myosin binding. Additionally, we have identified key residues of Tpm specifically binding to actins/myosin in the closed and open state. Some of them were validated as functionally important in comparison with past functional/clinical studies, and the rest will make promising targets for future mutational experiments.

Ionic Liquid-Controlled Growth of NiCo2 S4 3D Hierarchical Hollow Nanoarrow Arrays on Ni Foam for Superior Performance Binder Free Hybrid Supercapacitors.

A significant development in the design of a NiCo2 S4 3D hierarchical hollow nanoarrow arrays (HNA)-based supercapacitor binder free electrode assembled by 1D hollow nanoneedles and 2D nanosheets on a Ni foam collector through controlling ionic liquid 1-octyl-3-methylimidazolium chloride ([OMIm]Cl) concentration is reported. The unique NiCo2 S4 -HNA electrode acquires high specific capacity (1297 C g-1 at 1 A g-1 , 2.59 C cm-2 at 2 mA cm-2 ), excellent rate capability (maintaining 73.0% at 20 A g-1 ), and long operational life (maintaining 92.4% after 10 000 cycles at 5 A g-1 ), which are superior to those for 1D hollow nanoneedle arrays (HNN) and 2D porous nanoflake arrays (PNF). The outstanding electrochemical performance is attributed to the novel 3D structure with large specific surface, hollow cores, high porosity as well as stable architecture. In addition, a hybrid supercapacitor applying 3D NiCo2 S4 -HNA as the positive electrode and active carbon as the negative electrode exhibits a high energy density of 42.5 Wh kg-1 at a power density of 2684.2 W kg-1 in an operating voltage of 1.6 V. Robust cycling stability is also expressed with 84.9% retention after repeating 10 000 cycles at 5 A g-1 , implying their great potential in superior-performance supercapacitors.

Decrypting the Heat Activation Mechanism of TRPV1 Channel by Molecular Dynamics Simulation.

As a prototype cellular sensor, the TRPV1 cation channel undergoes a closed-to-open gating transition in response to various physical and chemical stimuli including noxious heat. Despite recent progress, the molecular mechanism of heat activation of TRPV1 gating remains enigmatic. Toward decrypting the structural basis of TRPV1 heat activation, we performed extensive molecular dynamics simulations (with cumulative simulation time of ∼11 µs) for the wild-type channel and a constitutively active double mutant at different temperatures (30, 60, and 72°C), starting from a high-resolution closed-channel structure of TRPV1 solved by cryo-electron microscopy. In the wild-type simulations, we observed heat-activated conformational changes (e.g., expansion or contraction) in various key domains of TRPV1 (e.g., the S2-S3 and S4-S5 linkers) to prime the channel for gating. These conformational changes involve a number of dynamic hydrogen-bond interactions that were validated with previous mutational studies. Next, our mutant simulations observed channel opening after a series of conformational changes that propagate from the channel periphery to the channel pore via key intermediate domains (including the S2-S3 and S4-S5 linkers). The gating transition is accompanied by a large increase in the protein-water electrostatic interaction energy, which supports the contribution of desolvation of polar/charged residues to the temperature-sensitive TRPV1 gating. Taken together, our molecular dynamics simulations and analyses offered, to our knowledge, new structural, dynamic, and energetic information to guide future mutagenesis and functional studies of the TRPV1 channels and development of TRPV1-targeting drugs.

Pathogenic mechanism of a catecholaminergic polymorphic ventricular tachycardia causing-mutation in cardiac calcium release channel RyR2.

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a condition that is characterized by an abnormal heart rhythm in response to physical or emotional stress. The majority CPVT patients carry mutations in the RYR2 gene that encodes the calcium release channel/ryanodine receptor (RyR2) in cardiomyocytes. The pathogenic mechanisms that account for the clinical phenotypes of CPVT are still elusive. We have identified a de novo mutation, A165D, from a CPVT patient. We found that CPVT phenotypes are recapitulated in A165D knock-in mice. The mutant RyR2 channels enhanced sarcoplasmic reticulum Ca2+ release, triggered delayed afterdepolarization in cardiomyocytes. Structural analysis revealed that the A165D mutation is located in a loop that is involved in inter-subunit interactions in the RyR2 tetrameric structure, it disrupted conformational stability of the RyR2, which favored a closed-to-open state transition, resulting in a leaky channel. The loop also harbors several other CPVT mutations, which suggests a common pathogenic molecular mechanism of CPVT-causing mutations. Our data illustrated disease-relevant functional defects and provide a deeper mechanistic understanding of a life-threatening cardiac arrhythmia.