Molecular mechanism for target recognition, dimerization, and activation of Pyrococcus furiosus Argonaute.

The Argonaute nuclease from the thermophilic archaeon Pyrococcus furiosus (PfAgo) contributes to host defense and represents a promising biotechnology tool. Here, we report the structure of a PfAgo-guide DNA-target DNA ternary complex at the cleavage-compatible state. The ternary complex is predominantly dimerized, and the dimerization is solely mediated by PfAgo at PIWI-MID, PIWI-PIWI, and PAZ-N interfaces. Additionally, PfAgo accommodates a short 14-bp guide-target DNA duplex with a wedge-type N domain and specifically recognizes 5'-phosphorylated guide DNA. In contrast, the PfAgo-guide DNA binary complex is monomeric, and the engagement of target DNA with 14-bp complementarity induces sufficient dimerization and activation of PfAgo, accompanied by movement of PAZ and N domains. A closely related Argonaute from Thermococcus thioreducens adopts a similar dimerization configuration with an additional zinc finger formed at the dimerization interface. Dimerization of both Argonautes stabilizes the catalytic loops, highlighting the important role of Argonaute dimerization in the activation and target cleavage.

Construction of Phosphorothiolated 2-Pyrrolidinones via Photoredox/Copper-Catalyzed Cascade Radical Cyclization/Phosphorothiolation.

A photoredox/copper-catalyzed cascade radical cyclization/phosphorothiolation reaction of N-allylbromoacetamides and P(O)SH compounds has been established. A broad range of novel nonfluorine- or difluoro-substituted 2-pyrrolidinones bearing the C(sp3)-SP(O)(OR)2 moiety can be conveniently constructed in moderate to good yields under mild conditions. Importantly, most of the tested phosphorothiolated 2-pyrrolidinones showed potent inhibitory effects toward both AChE and BChE.

A programmable pAgo nuclease with RNA target preference from the psychrotolerant bacterium Mucilaginibacter paludis.

Argonaute (Ago) proteins are programmable nucleases found in eukaryotes and prokaryotes. Prokaryotic Agos (pAgos) share a high degree of structural homology with eukaryotic Agos (eAgos), and eAgos originate from pAgos. Although eAgos exclusively cleave RNA targets, most characterized pAgos cleave DNA targets. This study characterized a novel pAgo, MbpAgo, from the psychrotolerant bacterium Mucilaginibacter paludis which prefers to cleave RNA targets rather than DNA targets. Compared to previously studied Agos, MbpAgo can utilize both 5'phosphorylated(5'P) and 5'hydroxylated(5'OH) DNA guides (gDNAs) to efficiently cleave RNA targets at the canonical cleavage site if the guide is between 15 and 17 nt long. Furthermore, MbpAgo is active at a wide range of temperatures (4-65°C) and displays no obvious preference for the 5'-nucleotide of a guide. Single-nucleotide and most dinucleotide mismatches have no or little effects on cleavage efficiency, except for dinucleotide mismatches at positions 11-13 that dramatically reduce target cleavage. MbpAgo can efficiently cleave highly structured RNA targets using both 5'P and 5'OH gDNAs in the presence of Mg2+ or Mn2+. The biochemical characterization of MbpAgo paves the way for its use in RNA manipulations such as nucleic acid detection and clearance of RNA viruses.

A bacterial Argonaute from Tepiditoga spiralis with the ability of RNA guided plasmid cleavage.

The eukaryotic Argonaute proteins (eAgos) play an important role in the RNA interference pathway. The function and mechanism of prokaryotic Argonaute proteins (pAgos) in vivo are still unclear although the structure of pAgos and eAgos are highly homologous. Most of the reported pAgos have a preference for 5'P-gDNA, but MpAgo originated from bacteria Marinitoga piezophila preferentially uses 5'OH-gRNA to target DNA and RNA. To enrich our knowledge of this type of Argonaute proteins, here we report an Argonaute protein derived from Tepiditoga spiralis (TsAgo). Like MpAgo, TsAgo has a preference for 5'OH-gRNA. Meanwhile, TsAgo has DNA and RNA cleavage activity in presence of Mn2+ and Mg2+, and TsAgo has catalytic activity at 37-70 °C. In addition, TsAgo can tolerate mismatches in the 5'-end and 3'-tail regions of guides but is sensitive to mismatches in the 5'-seed and central regions of guides, especially the central region. Furthermore, the EMSA assay reveals that TsAgo exhibits a stronger binding affinity for 5'OH-gRNA than 5'P-gRNA which is consistent with its cleavage activity. Moreover, the structural modeling analysis demonstrates that like MpAgo, TsAgo has an ordered α5 at the C terminus of the PIWI domain which may hinder to binding of 5' phosphate. Importantly, we find that TsAgo can target and cut plasmid DNA in vitro at 60 °C under the direction of RNA guides. These studies broaden our understanding of pAgos, and demonstrate that TsAgo can be regarded as an RNA-guided programmable nuclease for cleaving plasmids.

A programmable omnipotent Argonaute nuclease from mesophilic bacteria Kurthia massiliensis.

Argonaute (Ago) proteins are conserved nucleic acid-guided proteins present in all domains of life. Eukaryotic Argonaute proteins (eAgos) are key players in RNA interference pathways and function as RNA-guided RNA endonucleases at physiological temperatures. Although eAgos are considered to evolve from prokaryotic Argonaute proteins (pAgos), previously studied pAgos were unable to catalyze RNA-guided RNA cleavage at physiological temperatures. Here, we describe a distinctive pAgo from mesophilic bacteria Kurthia massiliensis (KmAgo). KmAgo utilizes DNA guides to cleave single-stranded DNA (ssDNA) and RNA targets with high activity. KmAgo also utilizes RNA guides to cleave ssDNA and RNA targets at moderate temperatures. We show that KmAgo can use 5' phosphorylated DNA guides as small as 9-mers to cut ssDNA and RNA, like Clostridium butyricum Ago. Small DNA binding confers remarkable thermostability on KmAgo, and we can suppress the guide-independent plasmid processing activity of empty KmAgo by elevating the DNA guide loaded temperature. Moreover, KmAgo performs programmable cleavage of double-stranded DNA and highly structured RNA at 37°C. Therefore, KmAgo can be regarded as a DNA-guided programmable omnipotent nuclease for cleaving most types of nucleic acids efficiently. This study broadens our understanding of Ago proteins and could expand the pAgo-based DNA and RNA manipulation toolbox.

A Density-Based Multilevel Terrain-Adaptive Noise Removal Method for ICESat-2 Photon-Counting Data.

The photon point clouds collected by the high-sensitivity single-photon detector on the Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) are utilized in various applications. However, the discretely distributed noise among the signal photons greatly increases the difficulty of signal extraction, especially the edge noise adjacent to signals. To detect signal photons from vegetation coverage areas at different slopes, this paper proposes a density-based multilevel terrain-adaptive noise removal method (MTANR) that identifies noise in a coarse-to-fine strategy based on the distribution of noise photons and is evaluated with high-precision airborne LiDAR data. First, the histogram-based successive denoising method was used as a coarse denoising process to remove distant noise and part of the sparse noise, thereby increasing the fault tolerance of the subsequent steps. Second, a rotatable ellipse that adaptively corrects the direction and shape based on the slope was utilized to search for the optimal filtering direction (OFD). Based on the direction, sparse noise removal was accomplished robustly using the Otsu's method in conjunction with the ordering points to identify the clustering structure (OPTICS) and provide a nearly noise-free environment for edge searching. Finally, the edge noise was removed by near-ground edge searching, and the signal photons were better preserved by the surface lines. The proposed MTANR was validated in four typical experimental areas: two in Baishan, China, and two in Taranaki, New Zealand. A comparison was made with three other representative methods, namely differential, regressive, and Gaussian adaptive nearest neighbor (DRAGANN), used in ATL08 products, local distance statistics (LDS), and horizontal ellipse-based OPTICS. The results demonstrated that the values of the F1 score for the signal photon identification achieved by the proposed MTANR were 0.9762, 0.9857, 0.9839, and 0.9534, respectively, which were higher than those of the other methods mentioned above. In addition, the qualitative and quantitative results demonstrated that MTANR outperformed in scenes with steep slopes, abrupt terrain changes, and uneven vegetation coverage.

Bacteria-Mediated Tumor Therapy via Photothermally-Programmed Cytolysin A Expression.

By leveraging the ability of bacteria to express therapeutic protein cytolysin A (ClyA) through plasmid transformation, a thermally-activated biohybrid (TAB@Au) is constructed by biomineralizing gold nanoparticles (AuNPs) on the E. coli surface. Due to the feature of anaerobic bacteria homing to tumor microenvironments, the bacteria-based antitumor vehicles can be efficaciously accumulated at tumor sites. Under NIR laser irradiation, the biomineralized AuNPs harvest transdermal photons and convert them into local heat for photothermal therapy. After that, the produced heat elicits the expression of ClyA for killing tumor cells. In vitro and in vivo experiments verify the conception that the current therapeutic modality greatly inhibits the proliferation of tumor cells. In terms of the spatial specificity and non-invasiveness of NIR laser, the bacteria-based phototherapy represents an appealing way for tumor therapy.

Palladium-Catalyzed Cascade Difluoroalkylation and Phosphinoylation of 2-Vinyloxy Arylalkynes: Selective Synthesis of Difluoroalkyl-Containing Tetrasubstituted Alkenylphosphine Oxides.

A Pd-catalyzed difluoroalkylation/cyclization/phosphinoylation of 2-vinyloxy arylalkynes with ethyl difluoroiodoacetate and diarylphosphine oxides has been successfully developed. This reaction allows the formation of Csp3-CF2, Csp3-Csp2, and Csp2-P(O) bonds in one step, providing a straightforward route to difluoroalkyl-containing tetrasubstituted alkenylphosphine oxides with complete stereoselectivities under mild conditions.

Combination of ultrashort PCR and Pyrococcus furiosus Argonaute for DNA detection.

A simple and user-friendly nucleic acid sensing platform with 10 aM sensitivity, named USPCRP (combines ultrashort PCR with Pyrococcus furiosus Argonaute cleavage for nuleic acids detection) is reported. The product of this ultrashort PCR could be directly used as a DNA guide to mediate PfAgo cleavage of molecular beacons.

5-hydroxytryptamine 2C/1A receptors modulate the biphasic dose response of the head twitch response and locomotor activity induced by DOM in mice.

RATIONALE: The phenylalkylamine hallucinogen (-)-2,5-dimethoxy-4-methylamphetamine (DOM) exhibits an inverted U-shaped dose-response curve for both head twitch response (HTR) and locomotor activity in mice. Accumulated studies suggest that HTR and locomotor hyperactivity induced by DOM are mainly caused by the activation of serotonin 5-hydroxytryptamine 2 A receptor (5-HT2A receptor). However, the mechanisms underlying the biphasic dose response of HTR and locomotor activity induced by DOM, particularly at high doses, remain unclear. OBJECTIVES: The primary objective of this study is to investigate the modulation of 5-HT2A/2C/1A receptors in HTR and locomotor activity, while also exploring the potential receptor mechanisms underlying the biphasic dose response of DOM. METHODS: In this study, we employed pharmacological methods to identify the specific 5-HT receptor subtypes responsible for mediating the biphasic dose-response effects of DOM on HTR and locomotor activity in C57BL/6J mice. RESULTS: The 5-HT2A receptor selective antagonist (R)-[2,3-di(methoxy)phenyl]-[1-[2-(4-fluorophenyl)ethyl]piperidin-4-yl]methanol (M100907) (500 µg/kg, i.p.) fully blocked the HTR at every dose of DOM (0.615-10 mg/kg, i.p.) in C57BL/6J mice. M100907 (50 µg/kg, i.p.) decreased the locomotor hyperactivity induced by a low dose of DOM (0.625, 1.25 mg/kg, i.p.), but had no effect on the locomotor hypoactivity induced by a high dose of DOM (10 mg/kg) in C57BL/6J mice. The 5-HT2C antagonist 6-chloro-5-methyl-1-[(2-[2-methylpyrid-3yloxy]pyrid-5yl)carbamoyl]indoline (SB242084) (0.3, 1 mg/kg, i.p.) reduced the HTR induced by a dose of 2.5 mg/kg DOM, but did not affect the response to other doses. SB242084 (1 mg/kg, i.p.) significantly increased the locomotor activity induced by DOM (0.615-10 mg/kg, i.p.) in mice. The 5-HT1A antagonist N-[2-[4-(2-methoxyphenyl)-1-piperazinyl]ethyl]N-(2-pyridinyl) cyclohexane carboxamide maleate (WAY100635) (1 mg/kg, i.p.) increased both HTR and locomotor activity induced by DOM in mice. The 5-HT1A agonist 8-hydroxy-2-(di-n-propylamino)tetralin (8-OH-DPAT) (1 mg/kg, i.p.) significantly reduced both the HTR and locomotor activity induced by DOM in mice. Additionally, pretreatment with the Gαi/o inhibitor PTX (0.25 µg/mouse, i.c.v.) enhanced the HTR induced by DOM and attenuated the effect of DOM on locomotor activity in mice. CONCLUSIONS: Receptor subtypes 5-HT2C and 5-HT1A are implicated in the inverted U-shaped dose-response curves of HTR and locomotor activity induced by DOM in mice. The biphasic dose-response function of HTR and locomotor activity induced by DOM has different mechanisms in mice.

Preamplification-free ultra-fast and ultra-sensitive point-of-care testing via LwaCas13a.

CRISPR based nucleic acid detection technology provides a deployable approach to point of care testing. While, there remain challenges limiting its practical applications, such as the need for pre-amplification and the long turnaround time. Here, we present a self-cascade signal amplification method with LwaCas13a and an artificially designed "U" rich RNA of stem-loop structure (URH) for pre-amplification-free ultra-fast and ultra-sensitive point-of-care testing (PASSPORT). The PASSPORT system contains: URH, crRNA targeted the URH, crRNA targeted the interesting RNA, fluorescent RNA reporter and LwaCas13a. The assay realized the detection of 100 copies/mL, within 5 min. The PASSPORT platform was further adopted for the detection of marker gene from SASR-CoV-2 and Severe fever with thrombocytopenia syndrome virus (SFTSV), respectively, and 100% accuracy for the analysis of clinical specimens (100 SASR-CoV-2 specimens and 16 SFTSV specimens) was obtained. Integrated with a lateral flow assay device, this assay could provide an alternative platform for the development of point of care testing (POCT) biosensors. PASSPORT has the potential to enable sensitive, specific, user-friendly, rapid, affordable, equipment-free and point-of-care testing for the purpose of large-scale screening and in case of epidemic outbreak.

Branched hydrophobic tails in lipid nanoparticles enhance mRNA delivery for cancer immunotherapy.

Efficient and safe delivery of vulnerable mRNA is a long-standing challenge for the broad application of the emerging mRNA-based therapeutics. Herein, a combinatorial library containing 119 novel lipids was constructed via sequential aza-Michael addition reactions of arylates and varying amines to tackle the ongoing challenge in mRNA delivery. Through in vitro screening of the lipid library on IGROV 1 cells, we identified several synthetic lipids with superior mRNA delivery efficacy. The delivery capability of these lipids was verified by the potent expression of luciferase in BALB/c mice upon intravenous administration of luciferase-encoding mRNA lipid nanoparticles (LNPs). Further investigations on the structure-activity relationship revealed that lipids with branched hydrophobic tails were better at delivering mRNA than those containing linear tails at the similar total number of carbons. In comparison to linear tails, the branched tails endowed LNPs with less inner hydrophobicity, fewer surface charges, and proper stability, which benefits the cellular uptake of LNPs and the intracellular trafficking of mRNA, thus improves the delivery efficacy of mRNA. The therapeutical potential of the lead LNPs was evaluated by delivering ovalbumin (OVA)-encoding mRNA to mice bearing B16-OVA melanoma tumors. The results demonstrated that the administration of OVA mRNA LNPs significantly activated CD8+ T cells in tumor microenvironment and substantially prohibited the growth of the aggressive B16-OVA tumors. The robust antitumor efficacy highlights the great potential of these LNPs in cancer immunotherapy.

Metal-organic framework-mediated construction of confined ultrafine nickel phosphide immobilized in reduced graphene oxide with excellent cycle stability for asymmetric supercapacitors.

Transition metal phosphides (TMPs) with unique metalloid features have been promised great application potential in developing high-efficiency electrode materials for electrochemical energy storage. Nevertheless, sluggish ion transportation and poor cycling stability are the critical hurdles limiting their application prospects. Herein, we presented the metal-organic framework-mediated construction of ultrafine Ni2P immobilized in reduced graphene oxide (rGO). Nano-porous two-dimensional (2D) Ni-metal-organic framework (Ni-MOF) was grown on holey graphene oxide (Ni(BDC)-HGO), followed by MOF-mediated tandem pyrolysis (carbonization and phosphidation; Ni(BDC)-HGO-X-P, X denoted carbonization temperature and P represented phosphidation). Structural analysis revealed that the open-framework structure in Ni(BDC)-HGO-X-Ps had endowed them with excellent ion conductivity. The Ni2P wrapped by carbon shells and the PO bonds linking between Ni2P and rGO ensured the better structural stability of Ni(BDC)-HGO-X-Ps. The resulting Ni(BDC)-HGO-400-P delivered a capacitance of 2333.3 F g-1 at 1 A g-1 in a 6 M KOH aqueous electrolyte. More importantly, Ni(BDC)-HGO-400-P//activated carbon, the assembled asymmetric supercapacitor with an energy density of 64.5 Wh kg-1 and a power density of 31.7 kW kg-1, almost maintained its initial capacitance after 10,000 cycles. Furthermore, in situ electrochemical-Raman measurements were exploited to demonstrate the electrochemical changes of Ni(BDC)-HGO-400-P throughout the charging and discharging processes. This study has further shed light on the design rationality of TMPs for optimizing supercapacitor performance.

Red mud-derived iron carbon catalyst for the removal of organic pollutants in wastewater.

In order to reduce the environmental hazards of red mud (RM) and realize its resource utilization, in this study, RM-based iron-carbon micro-electrolysis material (RM-MEM) were prepared by a carbothermal reduction process using RM as raw material. The influence of the preparation conditions on the phase transformation and structural characteristics of the RM-MEM were investigated during the reduction process. The ability of RM-MEM to remove organic pollutants from wastewater was evaluated. The results showed that RM-MEM prepared at a reduction temperature of 1100 °C, a reduction time of 50 min and a coal dosage of 50% had the best removal effect for the degradation of methylene blue (MB). When the initial MB concentration was 20 mg L-1, the amount of RM-MEM material was 4 g L-1, the initial pH was 7, and the degradation efficiency reached 99.75% after 60 min. When RM-MEM is split into carbon free and iron free parts for use, the degradation effect becomes worse. Compared to other materials, RM-MEM has lower cost and better degradation. X-ray diffraction (XRD) analysis showed that hematite was transformed to zero-valent iron with the increase in the roasting temperature. Scanning electron microscopy (SEM) and energy spectroscopy (EDS) analysis showed that micron-sized ZVI particles were formed in the RM-MEM, and increasing the carbon thermal reduction temperature was beneficial to the growth of zero-valent iron particles.

GO/iron series systems enhancing the pH shock resistance of anaerobic systems for sulfate-containing organic wastewater treatment.

In this study, the effect of pH shock during the treatment of sulfate-containing organic wastewater was investigated using an anaerobic fermentation system reinforced with graphene oxide (GO)/iron series systems. The results show that the anaerobic system with the GO/iron series systems exhibited enhanced resistance to pH shock. Among them, the GO/Fe0 system had the strongest resistance to pH shock, the systems of GO/Fe3O4 and GO/Fe2O3 followed close behind, while the blank system performed the worst. After pH shock, the CODCr removal rate, SO4 2- removal rate, and gas production of the GO/Fe0 group were significantly improved compared with those of the control group by 51.0%, 65.3%, and 34.6%, respectively, while the accumulation of propionic acid was the lowest. Further, detailed microbial characterization revealed that the introduction of the GO/iron series systems was beneficial to the formation of more stable anaerobic co-metabolic flora in the system, and the relative abundance of Geobacter, Clostridium, Desulfobulbus and Desulfovibrio increased after acidic and alkaline shock.

Bacteria-Elicited Specific Thrombosis Utilizing Acid-Induced Cytolysin A Expression to Enable Potent Tumor Therapy.

Given the special microenvironment of solid tumors, live microorganisms have emerged as drug delivery vehicles and therapeutic agents. Here, an acid-induced therapeutic platform is constructed using attenuated Escherichia coli to express the cytolysin A protein. The bacteria can target and colonize tumor tissues without causing notable host toxicity. Bacterial infection can disrupt blood vessels and trigger thrombosis in tumor tissues, resulting in the cut-off of nutrient supply to tumor cells and the arrest of tumor growth. The expression of cytolysin A induced by the acidic tumor microenvironment further strengthens thrombosis and provides a complementary therapeutic option due to its pore-forming function. In a xenograft mouse tumor model, this strategy reduces tumor proliferation by 79% and significantly prevents tumor metastasis, thus paving a new avenue for bacteria-based tumor therapy.

Improved paclitaxel delivery with PEG-b-PLA/zein nanoparticles prepared via flash nanoprecipitation.

Polymeric micelle is a promising vehicle to improve the bioavailability and clinical outcomes of paclitaxel (PTX) which has been proven effective in the treatment of a wide range of cancers. However, conventional PTX formulation with the amphiphilic PEG-b-PLA usually suffers from insufficient PTX loading, low stability of PTX-micelles, and rapid PTX release due to low compatibility between PTX and PLA, limiting its clinical application. In this study, a novel nanoparticle platform was developed to improve the stability of PTX-loaded nanoparticles (NPs) and the delivery efficacy of PTX by integrating the flash nanoprecipitation (FNP) technique and a combination of amphiphilic PEG-PLA and super hydrophobic zein. The incorporation of zein led to the formation of distinct hydrophobic interiors of NPs which enhanced the interaction between PTX and NPs, therefore improving the encapsulation efficiency of PTX and sustained drug release compared with PEG-PLA micelles without zein. In addition, FNP allowed facile fabrication of PTX-NPs with smaller sizes and higher stability. These PTX-NPs showed superior sustained release of PTX and good cancer cell-killing in vitro. Among them, PTX-5k-16k-1Z NPs exhibited excellent biosafety and anti-tumor efficacy in a xenograft tumor model in mice, suggesting great potential in the delivery of hydrophobic drugs for cancer therapy.

A bacterial Argonaute with efficient DNA and RNA cleavage activity guided by small DNA and RNA.

Argonaute proteins are widespread in prokaryotes and eukaryotes with diversified catalytic activities. Here, we describe an Argonaute from Marinitoga hydrogenitolerans (MhAgo) with all eight cleavage activities. Utilization of all four types of guides and efficient cleavage of single-stranded DNA (ssDNA) and RNA targets are revealed. The preference for the 5'-terminus nucleotides of 5'P guides, but no obvious preferences for that in 5'OH guides, is further uncovered. Moreover, the cleavage efficiency is heavily impaired by mismatches in the central and 3'-supplementary regions of guides, and the affinity between guides or guides/target duplex and MhAgo is proved as one of the factors affecting cleavage efficiency. Structural and mutational analyses imply some unknown distinctive structural features behind the cleavage activity of MhAgo. Meanwhile, 5'OH-guide RNA (gRNA)-mediated plasmid cleavage activity is unveiled. Conclusively, MhAgo is versatile, and its biochemical characteristics improve our understanding of pAgos and the pAgo-based techniques.

The effects of temperature shock on the treatment of high-concentration organic wastewater by an Fe0/GO-anaerobic system.

In order to make up for the defects of traditional anaerobic fermentation systems, such as low energy utilization rates and the slow growth and reproduction of microorganisms, an Fe0/GO (zero-valent iron/graphene oxide) anaerobic biological treatment system was used as a treatment process in this paper, and the impact of temperature shock on the system during the treatment of high-concentration organic wastewater was studied. The experimental results showed that temperature shock reduced the CODCr removal rate and gas production level in each system, but the Fe0/GO group maintained a higher level and had the highest CODCr degradation rate after shocking. After temperature shock, the acetic acid content in each system was higher (above 90%), and the volatile fatty acid (VFA) content in the Fe0/GO group was the lowest. The mixed liquor suspended solids (MLSS) in all systems decreased after impact; the decrease was less in the Fe0/GO group and the increase was largest after temperature recovery. After shocking, the extracellular polymer substance (EPS) protein (PN) and polysaccharide (PS) levels in each system were both low. After temperature recovery, the PN/PS ratio of the Fe0/GO group was the highest, showing a strong impact resistance to temperature.