Structures of SenB and SenA enzymes from Variovorax paradoxus provide insights into carbon-selenium bond formation in selenoneine biosynthesis.

Selenoneine, an ergothioneine analog, is important for antioxidation and detoxification. SenB and SenA are two crucial enzymes that form carbon-selenium bonds in the selenoneine biosynthetic pathway. To investigate their underlying catalytic mechanisms, we obtained complex structures of SenB with its substrate UDP-N-acetylglucosamine (UDP-GlcNAc) and SenA with N-α-trimethyl histidine (TMH). SenB adopts a type-B glycosyltransferase fold. Structural and functional analysis of the interaction network at the active center provide key information on substrate recognition and suggest a metal-ion-independent, inverting mechanism is utilized for SenB-mediated selenoglycoside formation. Moreover, the complex structure of SenA with TMH and enzymatic activity assays highlight vital residues that control substrate binding and specificity. Based on the conserved structure and substrate-binding pocket of the type I sulfoxide synthase EgtB in the ergothioneine biosynthetic pathway, a similar reaction mechanism was proposed for the formation of C-Se bonds by SenA. The structures provide knowledge on selenoneine synthesis and lay groundwork for further applications of this pathway.

Phillyrin and its metabolites treat pulmonary embolism by targeting PLCß3 to inhibit platelet activation.

ETHNOPHARMACOLOGICAL RELEVANCE: Lian Qiao (LQ), the dried fruit of Forsythia suspensa (Thunb.) Vahl, is a well-documented traditional Chinese medicine known for its detoxifying and heat-clearing properties. Clinically, compounds containing LQ are widely used to treat thrombotic diseases, indicating that it may have antithrombotic effects. However, its exact mechanism of action remains unknown. AIM OF THE STUDY: This study aimed to verify the antithrombotic effect of LQ and further explore the material basis and target mechanism of its antithrombotic effect using various biological methods. MATERIALS AND METHODS: An epinephrine-collagen-thrombin-induced mouse model of acute pulmonary embolism (APE) was established to study the effects of LQ on thrombus development. A UPLC/Q/TOF-MS screening and identification system based on the inhibition of platelet aggregation and Ca2+ antagonism was established to determine the pharmacodynamic components of LQ that inhibit platelet activation. The inhibitory effect of active ingredients on platelet activation, and the determination of the target of their inhibitory effect on platelet activation have been studied using chemical proteomics. Furthermore, based on the structure and function of the target protein, a multidisciplinary approach was adopted to analyze the molecular mechanism of active ingredient binding to target proteins and to evaluate the effects of active ingredients on the downstream signaling pathways of target proteins. RESULTS: LQ showed significant anticoagulant effects in APE model mice. Phillyrin and phillygenin were the antiplatelet-activating components of LQ. PLCß3 was identified as a target for inhibiting platelet activation by phillyrin and its metabolites. The mechanism underlying the effect involves phillyrin and its metabolites inhibiting PLCß3 activity by blocking the binding of PLCß3 to Gαq through non-covalently targeting the ASN260 of PLCß3, thus inhibiting the downstream Gαq-PLCß3-Ca2+ signaling pathway, effectively hindering platelet activation and therefore playing an anticoagulant role. CONCLUSION: This study not only proposes and validates the antithrombotic effect of LQ for the first time but also finds that phillyrin and phillygenin are the main pharmacological substances through which LQ exerts antithrombotic activity and reveals a novel mechanism by which they exert antiplatelet activity by directly targeting and inhibiting PLCß3 activity. These findings significantly contribute to our understanding of the therapeutic potential of phillyrin and provide important clues for the discovery and development of new antiplatelet drugs.

Nickel-catalyzed regioselective hydrogen isotope exchange accelerated by 2-pyridones.

A nickel-catalyzed hydrogen isotope exchange has been developed with acetone-d6 as the deuterium source. The reaction showed an improved kinetic feature of H/D exchange under the assistance of 2-pyridones, efficiently affording regioselective labeled aryl and alkyl carboxamides.

Exogenous AMPA downregulates gamma-frequency network oscillation in CA3 of rat hippocampal slices.

Pharmacologically-induced persistent hippocampal γ oscillation in area CA3 requires activation of α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptors (AMPARs). However, we demonstrated that exogenous AMPA dose-dependently inhibited carbachol (CCH)-induced γ oscillation in the CA3 area of rat hippocampal slices, but the underlying mechanism is not clear. Application of AMPARs antagonist NBQX (1 µM) did not affect γ oscillation power (γ power), nor AMPA-mediated γ power reduction. At 3 µM, NBQX had no effect on γ power but largely blocked AMPA-mediated γ power reduction. Ca2+-permeable AMPA receptor (CP-AMPAR) antagonist IEM1460 or CaMKK inhibitor STO-609 but not CaMKIIα inhibitor KN93 enhanced γ power, indicating that activation of CP-AMPAR or CaMKK negatively modulated CCH-induced γ oscillation. Either CP-AMPAR antagonist or CaMKK inhibitor alone did not affected AMPA-mediated γ power reduction, but co-administration of IEM1460 and NBQX (1 µM) largely prevented AMPA-mediated downregulation of γ suggesting that CP-AMPARs and CI-AMPARs are involved in AMPA downregulation of γ oscillation. The recurrent excitation recorded at CA3 stratum pyramidale was significantly reduced by AMPA application. Our results indicate that AMPA downregulation of γ oscillation may be related to the reduced recurrent excitation within CA3 local neuronal network due to rapid CI-AMPAR and CP-AMPAR activation.

CRSExtractor: Automated configuration option read sites extraction towards IoT cloud infrastructure.

There are a large number of solutions for big data processing in the Internet of Things (IoT) environments, among which the IoT cloud infrastructure is one of the most mature solutions. Typically, modern IoT cloud infrastructures have different kinds of configuration options. The diversity of configurations leads to frequent software configuration errors. Generally, troubleshooting configuration errors relies on finding the mapping relationship between configuration options in the documents (e.g., official manuals) and their read sites in the source code. Most current works still manually extract configuration read sites. Automated methods are not always interchangeable and they incur considerable time overheads and low extraction rates. In this paper, we propose CRSExtractor, an automatic technique for extracting configuration read sites based on intra-procedural analysis. Using our technique, configuration option read sites can be automatically identified and built into maps with configuration options. Evaluations on several core software systems of IoT cloud platforms, such as Hadoop and Cassandra, show that our approach performs well, with an accuracy rate of over 90% and efficiency nearly 20 times faster than previous works.

Metapath-aggregated heterogeneous graph neural network for drug-target interaction prediction.

Drug-target interaction (DTI) prediction is an essential step in drug repositioning. A few graph neural network (GNN)-based methods have been proposed for DTI prediction using heterogeneous biological data. However, existing GNN-based methods only aggregate information from directly connected nodes restricted in a drug-related or a target-related network and are incapable of capturing high-order dependencies in the biological heterogeneous graph. In this paper, we propose a metapath-aggregated heterogeneous graph neural network (MHGNN) to capture complex structures and rich semantics in the biological heterogeneous graph for DTI prediction. Specifically, MHGNN enhances heterogeneous graph structure learning and high-order semantics learning by modeling high-order relations via metapaths. Additionally, MHGNN enriches high-order correlations between drug-target pairs (DTPs) by constructing a DTP correlation graph with DTPs as nodes. We conduct extensive experiments on three biological heterogeneous datasets. MHGNN favorably surpasses 17 state-of-the-art methods over 6 evaluation metrics, which verifies its efficacy for DTI prediction. The code is available at https://github.com/Zora-LM/MHGNN-DTI.

Brivaracetam Modulates Short-Term Synaptic Activity and Low-Frequency Spontaneous Brain Activity by Delaying Synaptic Vesicle Recycling in Two Distinct Rodent Models of Epileptic Seizures.

Brivaracetam (BRV) is an anti-seizure drug for the treatment of focal and generalized epileptic seizures shown to augment short-term synaptic fatigue by slowing down synaptic vesicle recycling rates in control animals. In this study, we sought to investigate whether altered short-term synaptic activities could be a pathological hallmark during the interictal periods of epileptic seizures in two well-established rodent models, as well as to reveal BRV's therapeutic roles in altered short-term synaptic activities and low-frequency band spontaneous brain hyperactivity in these models. In our study, the electrophysiological field excitatory post-synaptic potential (fEPSP) recordings were performed in rat hippocampal brain slices from the CA1 region by stimulation of the Schaffer collateral/commissural pathway with or without BRV (30 µM for 3 h) in control or epileptic seizure (induced by pilocarpine (PILO) or high potassium (h-K+)) models. Short-term synaptic activities were induced by 5, 10, 20, and 40-Hz stimulation sequences. The effects of BRV on pre-synaptic vesicle mobilization were visually assessed by staining the synaptic vesicles with FM1-43 dye followed by imaging with a two-photon microscope. In the fEPSP measurements, short-term synaptic fatigue was found in the control group, while short-term synaptic potentiation (STP) was detected in both PILO and h-K+ models. STP was decreased after the slices were treated with BRV (30 µM) for 3 h. BRV also exhibited its therapeutic benefits by decreasing abnormal peak power (frequency range of 8-13 Hz, 31% of variation for PILO model, 25% of variation for h-K+ model) and trough power (frequency range of 1-4 Hz, 66% of variation for PILO model, 49% of variation for h-K+ model), and FM1-43 stained synaptic vesicle mobility (64% of the variation for PILO model, 45% of the variation for h-K+ model) in these epileptic seizure models. To the best of our knowledge, this was the first report that BRV decreased the STP and abnormal low-frequency brain activities during the interictal phase of epileptic seizures by slowing down the mobilization of synaptic vesicles in two rodent models. These mechanistic findings would greatly advance our understanding of BRV's pharmacological role in pathomechanisms of epileptic seizures and its treatment strategy optimization to avoid or minimize BRV-induced possible adverse side reactions.

Extracellular proteins of Desulfovibrio vulgaris as adsorbents and redox shuttles promote biomineralization of antimony.

Biomineralization is the key process governing the biogeochemical cycling of multivalent metals in the environment. Although some sulfate-reducing bacteria (SRB) are recently recognized to respire metal ions, the role of their extracellular proteins in the immobilization and redox transformation of antimony (Sb) remains elusive. Here, a model strain Desulfovibrio vulgaris Hildenborough (DvH) was used to study microbial extracellular proteins of functions and possible mechanisms in Sb(V) biomineralization. We found that the functional groups (N-H, CO, O-CO, NH2-R and RCOH/RCNH2) of extracellular proteins could adsorb and fix Sb(V) through electrostatic attraction and chelation. DvH could rapidly reduce Sb(V) adsorbed on the cell surface and form amorphous nanometer-sized stibnite and/or antimony trioxide, respectively with sulfur and oxygen. Proteomic analysis indicated that some extracellular proteins involved in electron transfer increased significantly (p < 0.05) at 1.8 mM Sb(V). The upregulated flavoproteins could serve as a redox shuttle to transfer electrons from c-type cytochrome networks to reduce Sb(V). Also, the upregulated extracellular proteins involved in sulfur reduction, amino acid transport and protein synthesis processes, and the downregulated flagellar proteins would contribute to a better adaption under 1.8 mM Sb(V). This study advances our understanding of how microbial extracellular proteins promote Sb biomineralization in DvH.

Long-term effect of fulvic acid amendment on the anammox biofilm system at 15 ℃: performance, microbial community and metagenomics analysis.

The role of fulvic acid (FA) on the anammox system at 15 ℃ was investigated. After operation for 113 days, total inorganic nitrogen removal efficiency in FA amendment reactor achieved to 58.6% on average, higher than that of control group (42.1%). Anammox-related functional genes, i.e., hzo and hzs, also demonstrated higher expression level after introduction of FA. It was observed that Candidatus Kuenenia became more competitive than Candidatus Brocadia with the existence of FA at 15 ℃. Also, co-occurrence analysis showed that FA stimulated the complexity and interactive relationship of microbial communities in the anammox system. Metagenomics analysis revealed that FA introduction stimulated relative abundances of genes in central pathway of tricarboxylic acid cycle such as ACO, IDH, OGDH, SCS, FUM, and MDH. Meanwhile, metabolomics analysis revealed that metabolites related to amino sugar metabolic pathways (glucose 1-phosphate, UDP-D-glucuronate, UDP) and redox reactions (NAD+ and NADH) improved in the FA amendment reactor.

Effect of exogenous N-acyl-homoserine lactones on the anammox process at 15 ℃: Nitrogen removal performance, gene expression and metagenomics analysis.

In this study, C6-HSL and C8-HSL were separately introduced into anammox biofilm reactors to facilitate the anammox performance at 15 ℃. After operation 138 d, total nitrogen removal efficiencies in reactors with amendment C6-HSL or C8-HSL at 15 ℃ reached 76.2% and 74.6%, respectively. Content of extracellular polymeric substances increased by 19.8%, 67.7% and 121.2% in control group, C6-HSL and C8-HSL addition group, respectively. Genes associated with nitrogen removal (i.e., hzo, hzsB, nirS, and ccsB) showed higher expression level at amendment C6-HSL or C8-HSL group. Metagenomics analysis found that amendment of C6-HSL or C8-HL resulted in an increased abundance of genes related to the tricarboxylic acid cycle, amino sugar and nucleotide sugar metabolism, and also genes associated with amino acid biosynthesis pathways. Overall, amendment C6-HSL or C8-HSL had been confirmed as the effective method to improve the performance of anammox bioreactor at 15 ℃.

Woodchips bioretention column for stormwater treatment: Nitrogen removal performance, carbon source and microbial community analysis.

This study chose Oak woodchips and gravel as media filter to enhance the denitrification in the bioretention system (saturated zone 7.7 L) treating synthetic stormwater runoff. It revealed that the denitrification process mainly occurred during the drying phase and enlarging volume of saturated zones to retain more stormwater during storm event was the direct method to promote nitrogen removal of the bioretention system. Nevertheless, it was noted that the nitrogen and dissolved organic carbon would be released into the effluent during the wetting period. The denitrification rate with different nitrate nitrogen (NO3-N) concentrations did not show the obvious change with zero order kinetics constant of 2.91 mg/L∙d on average. Furthermore, it confirmed that woodchips were degraded and converted to volatile fatty acids (VFAs), especially acetic acid as carbon source, further utilized by the denitrifying bacteria, such as Dechloromonas, Acidoborax, Pseudomonas, Denitratisoma and Acinetobacter. In addition, genera of Lachnospiraceae and Lactobacillus, which had the ability to degrade the macromolecular organic components into low molecular VFAs, were observed in the woodchips bioretention system.

One-stage partial nitrification and anammox process in a sequencing batch biofilm reactor: Start-up, nitrogen removal performance and bacterial community dynamics in response to temperature.

A one-stage partial nitrification and anammox (PN/A) process was started up and operated under varying temperatures in a lab-scale sequencing batch biofilm reactor. The start­up phase took 110 days with an intermittent aeration strategy, and the removal efficiencies of ammonia­nitrogen and total nitrogen were found to be 92.22% and 76.07%, respectively. The total nitrogen removal efficiency (NRE) increased by 9.49% when temperature decreased from 30 °C to 25 °C, but declined by 83.84% from 25 °C to 20 °C. The PN process was inhibited and subsequently limited the nitrogen removal performance at 20 °C. When temperature returned to 28 °C, the NRE recovered to 67.27%, but it was still lower than the value before the decrease in temperature (79.40%). Microbial community analysis showed that the predominant ammonia oxidation bacteria and anammox bacteria were Nitrosomonas and Candidatus Kuenenia, respectively. Nitrosomonas grew, while the relative abundance of Candidatus Kuenenia increased as temperature decreased and vice versa.

Levetiracetam induction of theta frequency oscillations in rodent hippocampus in vitro.

Levetiracetam (LEV) has been demonstrated to improve cognitive function. Hippocampal theta rhythm (4-12 Hz) is associated with a variety of cognitively related behaviors, such as exploration in both humans and animal models. We investigated the effects of LEV on the theta rhythm in the rat hippocampal CA3 in hippocampal slices in vitro. We found that LEV increased the theta power in a dose-dependent manner. The increase in theta power can be blocked by GABAA receptor (GABAAR) or NMDA receptor (NMDAR) antagonists but not by AMPA receptor antagonist, indicating the involvement of GABAAR and NMDAR in the induction of theta activity. Interestingly, LEV enhancement of theta power can be also blocked by taurine or GABA-A agonist THIP, indicating that LEV induction of theta may be related to the indirect boosting of GABA action via reduction of extrasynaptic GABAAR activation. Furthermore, the increased theta power can be partially reduced by the mACh receptor (mAChR) antagonist atropine but not by nACh receptor antagonists, suggesting that mAChR activation provides excitatory input into local network responsible for LEV-induced theta. Our study demonstrated that LEV induced a novel theta oscillation in vitro, which may have implications in the treatment of the neuronal disorders with impaired theta oscillation and cognitive function.