Flow-Cell-Based Technology for Massively Parallel Characterization of Base-Modified DNA Aptamers.

Aptamers incorporating chemically modified bases can achieve superior affinity and specificity compared to natural aptamers, but their characterization remains a labor-intensive, low-throughput task. Here, we describe the "non-natural aptamer array" (N2A2) system, in which a minimally modified Illumina MiSeq instrument is used for the high-throughput generation and characterization of large libraries of base-modified DNA aptamer candidates based on both target binding and specificity. We first demonstrate the capability to screen multiple different base modifications to identify the optimal chemistry for high-affinity target binding. We next use N2A2 to generate aptamers that can maintain excellent specificity even in complex samples, with equally strong target affinity in both buffer and diluted human serum. For both aptamers, affinity was formally calculated with gold-standard binding assays. Given that N2A2 requires only minor mechanical modifications to the MiSeq, we believe that N2A2 offers a broadly accessible tool for generating high-quality affinity reagents for diverse applications.

Hedgehog pathway activation through nanobody-mediated conformational blockade of the Patched sterol conduit.

Activation of the Hedgehog pathway may have therapeutic value for improved bone healing, taste receptor cell regeneration, and alleviation of colitis or other conditions. Systemic pathway activation, however, may be detrimental, and agents amenable to tissue targeting for therapeutic application have been lacking. We have developed an agonist, a conformation-specific nanobody against the Hedgehog receptor Patched1 (PTCH1). This nanobody potently activates the Hedgehog pathway in vitro and in vivo by stabilizing an alternative conformation of a Patched1 "switch helix," as revealed by our cryogenic electron microscopy structure. Nanobody-binding likely traps Patched in one stage of its transport cycle, thus preventing substrate movement through the Patched1 sterol conduit. Unlike the native Hedgehog ligand, this nanobody does not require lipid modifications for its activity, facilitating mechanistic studies of Hedgehog pathway activation and the engineering of pathway activating agents for therapeutic use. Our conformation-selective nanobody approach may be generally applicable to the study of other PTCH1 homologs.

Lactobacillus plantarum strains attenuated DSS-induced colitis in mice by modulating the gut microbiota and immune response.

Gut microbiota has become a new therapeutic target in the treatment of inflammatory Bowel Disease (IBD). Probiotics are known for their beneficial effects and have shown good efficacy in the clinical treatment of IBD and animal models of colitis. However, how these probiotics contribute to the amelioration of IBD is largely unknown. In the current study, the DSS-induced mouse colitis model was treated with oral administration of Lactobacillus plantarum strains to investigate their effects on colitis. The results indicated that the L. plantarum strains improved dysbiosis and enhanced the abundance of beneficial bacteria related to short-chain fatty acids (SCFAs) production. Moreover, L. plantarum strains decreased the level of pro-inflammatory cytokines, i.e., IL-17A, IL-17F, IL-6, IL-22, and TNF-α and increased the level of anti-inflammatory cytokines, i.e., TGF-ß, IL-10. Our result suggests that L. plantarum strains possess probiotic effects and can ameliorate DSS colitis in mice by modulating the resident gut microbiota and immune response.

Antibacterial activity and action mechanism of flavonoids against phytopathogenic bacteria.

As the most difficult to control in plant disease, phytopathogenic bacteria cause huge losses to agricultural products and economy worldwide. However, the commercially available bactericides are few and enhance pathogen resistance. To alleviate this situation, 50 flavonoids were evaluated for their antibacterial activities and mechanism of action against two intractable plant bacterial pathogens. The results of bioassays showed that most of the flavonoids exhibited moderate inhibitory effects against Xanthomonas oryzae (Xo) and Xanthomonas axonopodis pv citri (Xac). Remarkably, kaempferol showed excellent antibacterial activity against Xo in vitro (EC50 = 15.91 µg/mL) and quercetin showed the best antibacterial activity against Xac in vitro (EC50 = 14.83 µg/mL), which was better than thiodiazole copper (EC50 values against Xo and Xac were 16.79 µg/mL, 59.13 µg/mL, respectively). Subsequently, in vivo antibacterial activity assay further demonstrated kaempferol exhibited a stronger control effect on bacterial infections than thiodiazole copper. Then, the preliminary antibacterial mechanism of kaempferol was investigated by ultrastructural observations, transcriptomic, qRT-PCR analysis and biochemical index determination. These results showed that kaempferol mainly exerted bacteriostatic effects at the molecular level by affecting bacterial energy metabolism, reducing pathogenicity, and leading to disruption of cellular integrity, leakage of contents and cell death eventually.

Efficacy Comparison of 3 Kinds of Distal Tibial Hemiepiphyseal Implants in the Treatment of Postoperative Ankle Valgus of Congenital Pseudarthrosis of the Tibia.

BACKGROUND: Congenital pseudarthrosis of the tibia (CPT) is a complex and serious disease in orthopaedics which often requires multiple operations for treatment. Postoperative ankle valgus deformity is easily seen after the operation of CPT. The aim of this study is to retrospectively evaluate the effectiveness of three different implants for treating postoperative ankle valgus after CPT. METHODS: A total of 41 patients with postoperative ankle valgus after CPT from December 2010 to July 2019 were selected. Of these 41 patients, 23 patients were treated with "U"-shaped staple, 10 patients were treated with hollow screw and 8 patients were treated with cortical bone screw. The evaluation index was tibiotalar angle. The general data, preoperative, postoperative, and final follow-up imaging data were recorded, and the deformity correction rate and complications were compared. RESULTS: All the patients were performed with postoperative follow-up visit for at least 12 months (31 mo on average). In the "U"-shaped staple group, the preoperative tibiotalar angle was 74.8±4.8 degrees, the tibiotalar angle was 85.8±4.5 degrees when the internal fixation was removed; in the hollow screw group, the average preoperative tibiotalar angle was 72.2±6.1 degrees, the average tibiotalar angle was 88.4±5.1 degrees when the internal fixation was removed; in the cortical bone screw group, the average preoperative tibiotalar angle was 75.1±4.2 degrees, the average tibiotalar angle was 88.4±5.1 degrees when the internal fixation was removed. The correction rate of the "U"-shaped staple group was 0.71 degrees/month, with that of in the hollow screw group and cortical bone screw group being 0.64 degrees/month and 0.61 degrees/month, respectively. There was no significant difference in the correction rate between the 3 groups. One case of internal fixation complication was reported in the hollow screw group; 2 cases of missing correction effect were reported, 1 in cortical bone screw group and 1 in hollow screw group; and 2 cases showing symptom of wound pain were reported in the "U"-shaped staple group. CONCLUSION: Ankle valgus is a common postoperative complication of congenital tibial pseudarthrosis. Temporary hemiepiphysiodesis with "U"-shaped staple or screws is an effective treatment for postoperative ankle valgus deformity of CPT in children. LEVEL OF EVIDENCE: Level IV-retrospective study.

Immune signature-based risk stratification and prediction of immune checkpoint inhibitor's efficacy for lung adenocarcinoma.

BACKGROUND: Lung adenocarcinoma (LUAD) is a common pulmonary malignant disease with a poor prognosis. There were limited studies investigating the influences of the tumor immune microenvironment on LUAD patients' survival and response to immune checkpoint inhibitors (ICIs). METHODS: Based on TCGA-LUAD dataset, we constructed a prognostic immune signature and validated its predictive capability in the internal as well as total datasets. Then, we explored the differences of tumor-infiltrating lymphocytes, tumor mutation burden, and patients' response to ICI treatment between the high-risk score group and low-risk score group. RESULTS: This immune signature consisted of 17 immune-related genes, which was an independent prognostic factor for LUAD patients. In the low-risk score group, patients had better overall survival. Although the differences were non-significant, patients with low-risk scores had more tumor-infiltrating follicular helper T cells and fewer macrophages (M0), which were closely related to clinical outcomes. Additionally, the total TMB was markedly decreased in the low-risk score group. Using immunophenoscore as a surrogate of ICI response, we found that patients with low-risk scores had significantly higher immunophenoscore. CONCLUSION: The 17-immune-related genes signature may have prognostic and predictive relevance with ICI therapy but needs prospective validation.

Atomically thin half-van der Waals metals enabled by confinement heteroepitaxy.

Atomically thin two-dimensional (2D) metals may be key ingredients in next-generation quantum and optoelectronic devices. However, 2D metals must be stabilized against environmental degradation and integrated into heterostructure devices at the wafer scale. The high-energy interface between silicon carbide and epitaxial graphene provides an intriguing framework for stabilizing a diverse range of 2D metals. Here we demonstrate large-area, environmentally stable, single-crystal 2D gallium, indium and tin that are stabilized at the interface of epitaxial graphene and silicon carbide. The 2D metals are covalently bonded to SiC below but present a non-bonded interface to the graphene overlayer; that is, they are 'half van der Waals' metals with strong internal gradients in bonding character. These non-centrosymmetric 2D metals offer compelling opportunities for superconducting devices, topological phenomena and advanced optoelectronic properties. For example, the reported 2D Ga is a superconductor that combines six strongly coupled Ga-derived electron pockets with a large nearly free-electron Fermi surface that closely approaches the Dirac points of the graphene overlayer.

Antifungal Activity and Action Mechanism Study of Coumarins from Cnidium monnieri Fruit and Structurally Related Compounds.

The increasing resistance of plant diseases caused by phytopathogenic fungi highlights the need for highly effective and environmentally benign agents. The antifungal activities of Cnidium monnieri fruit extracts and five isolated compounds as well as structurally related coumarins against five plant pathogenic fungi were evaluated. The acetone extract, which contained the highest amount of five coumarins, showed strongest antifungal activity. Among the coumarin compounds, we found that 4-methoxycoumarin exhibited stronger and broader antifungal activity against five phytopathogenic fungi, and was more potent than osthol. Especially, it could significantly inhibit the growth of Rhizoctonia solani mycelium with an EC50 value of 21 µg mL-1 . Further studies showed that 4-methoxycoumarin affected the structure and function of peroxisomes, inhibited the ß-oxidation of fatty acids, decreased the production of ATP and acetyl coenzyme A, and then accumulated ROS by damaging MMP and the mitochondrial function to cause the cell death of R. solani mycelia. 4-Methoxycoumarin presented antifungal efficacy in a concentration- dependent manner in vivo and could be used to prevent the potato black scurf. This study laid the foundation for the future development of 4-methoxycournamin as an alternative and friendly biofungicide.

Spin-Dependent Thermoelectric Power of Nanoislands.

The Seebeck effect explains the generation of electric voltage as a result of a temperature gradient. Its efficiency, defined as the ratio of the generated electric voltage to the temperature difference, is sensitive to local inhomogeneities that alter the scattering rate and the density of the conduction electrons. Spin-polarized Seebeck tunneling generates a distinct thermovoltage in spin-up and spin-down charge transport channels, which, as a key to spin caloritronics, focuses on transport phenomena related to spin and heat. Here, we report spatially resolved measurement of the spin-dependent thermovoltage in a tunneling junction formed by ferromagnetic Co nanoislands and a Ni tip using spin-dependent scanning tunneling thermovoltage microscopy (SP-STVthM). We resolve the nanoscale thermoelectric powers with respect to spin polarization, nanoisland size, stacking order of Co layers on a Cu substrate, and local sample heterogeneities. The observed thermally generated spin voltages are supported by first-principles and model calculations.

Facile Size-Selective Defect Sealing in Large-Area Atomically Thin Graphene Membranes for Sub-Nanometer Scale Separations.

Atomically thin graphene with a high-density of precise subnanometer pores represents the ideal membrane for ionic and molecular separations. However, a single large-nanopore can severely compromise membrane performance and differential etching between pre-existing defects/grain boundaries in graphene and pristine regions presents fundamental limitations. Here, we show for the first time that size-selective interfacial polymerization after high-density nanopore formation in graphene not only seals larger defects (>0.5 nm) and macroscopic tears but also successfully preserves the smaller subnanometer pores. Low-temperature growth followed by mild UV/ozone oxidation allows for facile and scalable formation of high-density (4-5.5 × 1012 cm-2) useful subnanometer pores in the graphene lattice. We demonstrate scalable synthesis of fully functional centimeter-scale nanoporous atomically thin membranes (NATMs) with water (∼0.28 nm) permeance ∼23× higher than commercially available membranes and excellent rejection to salt ions (∼0.66 nm, >97% rejection) as well as small organic molecules (∼0.7-1.5 nm, ∼100% rejection) under forward osmosis.

Fungicidal Activity and Mechanism of Action of Glabridin from Glycyrrhiza glabra L.

Glycyrrhiza glabra (Licorice) belongs to the Fabaceae family and its extracts have exhibited significant fungicidal activity against phytopathogenic fungi, which has mainly been attributed to the presence of phenolic compounds such as flavonoids, isoflavonoids and chalcones. In this study, a series of licorice flavonoids, isoflavonoids and chalcones were evaluated for their fungicidal activity against phytopathogenic fungi. Among them, glabridin exhibited significant fungicidal activity against ten kinds of phytopathogenic fungi. Notably, glabridin displayed the most active against Sclerotinia sclerotiorum with an EC50 value of 6.78 µg/mL and was 8-fold more potent than azoxystrobin (EC50, 57.39 µg/mL). Moreover, the in vivo bioassay also demonstrated that glabridin could effectively control S. sclerotiorum. The mechanism studies revealed that glabridin could induce reactive oxygen species accumulation, the loss of mitochondrial membrane potential and cell membrane destruction through effecting the expression levels of phosphatidylserine decarboxylase that exerted its fungicidal activity. These findings indicated that glabridin exhibited pronounced fungicidal activities against S. sclerotiorum and could be served as a potential fungicidal candidate.

Exceptional ballistic transport in epitaxial graphene nanoribbons.

Graphene nanoribbons will be essential components in future graphene nanoelectronics. However, in typical nanoribbons produced from lithographically patterned exfoliated graphene, the charge carriers travel only about ten nanometres between scattering events, resulting in minimum sheet resistances of about one kilohm per square. Here we show that 40-nanometre-wide graphene nanoribbons epitaxially grown on silicon carbide are single-channel room-temperature ballistic conductors on a length scale greater than ten micrometres, which is similar to the performance of metallic carbon nanotubes. This is equivalent to sheet resistances below 1 ohm per square, surpassing theoretical predictions for perfect graphene by at least an order of magnitude. In neutral graphene ribbons, we show that transport is dominated by two modes. One is ballistic and temperature independent; the other is thermally activated. Transport is protected from back-scattering, possibly reflecting ground-state properties of neutral graphene. At room temperature, the resistance of both modes is found to increase abruptly at a particular length--the ballistic mode at 16 micrometres and the other at 160 nanometres. Our epitaxial graphene nanoribbons will be important not only in fundamental science, but also--because they can be readily produced in thousands--in advanced nanoelectronics, which can make use of their room-temperature ballistic transport properties.

Synergistic effect of immune checkpoint blockade and anti-angiogenesis in cancer treatment.

Immune checkpoint inhibitor (ICI) activates host's anti-tumor immune response by blocking negative regulatory immune signals. A series of clinical trials showed that ICI could effectively induce tumor regression in a subset of advanced cancer patients. In clinical practice, a main concerning for choosing ICI is the low response rate. Even though multiple predictive biomarkers such as PD-L1 expression, mismatch-repair deficiency, and status of tumor infiltrating lymphocytes have been adopted for patient selection, frequent resistance to ICI monotherapy has not been completely resolved. However, some recent studies indicated that ICI resistance could be alleviated by combination therapy with anti-angiogenesis treatment. Actually, anti-angiogenesis therapy not only prunes blood vessel which is essential to cancer growth and metastasis, but also reprograms the tumor immune microenvironment. Preclinical studies demonstrated that the efficacy of combination therapy of ICI and anti-angiogenesis was superior to monotherapy. In mice model, combination therapy could effectively increase the ratio of anti-tumor/pro-tumor immune cell and decrease the expression of multiple immune checkpoints more than PD-1. Based on exciting results from preclinical studies, many clinical trials were deployed to investigate the synergistic effect of the combination therapy and acquired promising outcome. This review summarized the latest understanding of ICI combined anti-angiogenesis therapy and highlighted the advances of relevant clinical trials.

Tuning Magnetic Soliton Phase via Dimensional Confinement in Exfoliated 2D Cr1/3NbS2 Thin Flakes.

Thin flakes of Cr1/3NbS2 are fabricated successfully via microexfoliation techniques. Temperature-dependent and field-dependent magnetizations of thin flakes with various thicknesses are investigated. When the thickness of the flake is around several hundred nanometers, the softening and eventual disappearance of the bulk soliton peak is accompanied by the appearance of other magnetic peaks at lower magnetic fields. The emergence and annihilation of the soliton peaks are explained and simulated theoretically by the change in spin spiral number inside the soliton lattice due to dimensional confinement. Compared to the conventional magnetic states in nanoscale materials, the stability and thickness tunability of quantified spin spirals make Cr1/3NbS2 a potential candidate for spintronics nanodevices beyond Moore's law.

[Determination of forbidden and restricted pesticides in Angelicae Sinensis Radix].

The present study is to establish a method for simultaneous determination of 50 kinds of pesticides in Angelicae Sinensis Radix by using liquid chromatography tandem mass spectrometry. The forbidden,restricted and customary pesticides were picked out as detecting indexes according to the principals of risk management. The factors affecting the extraction,purification,and detection were optimized,and the final condition was established as follows: the samples were extracted with acetonitrile. The separation of target compounds were performed by liquid column,and quantitative analysis was carried out by LC-MS/MS with MRM model. The calibration curves were linear in the range of 1-100 µg·L~(-1) with correction coefficients of greater than 0. 990. The recoveries of more than 93. 9%pesticides were ranged from 60% to 140% at three spiked levels. The detecting indexes in the method cover most forbidden and restricted pesticides,which is meaningful for the safety supervision of the Angelicae Sinensis Radix. With the advantage of rapidness and accuracy,this method can be used for routine determination of multi-pesticides in Angelicae Sinensis Radix.

Accessing the Intrinsic Spin Transport in a Topological Insulator by Controlling the Crossover of Bulk-to-Surface Conductance.

We report a method to control contributions of bulk and surface states in the topological insulator Bi_{2}Te_{2}Se that allows accessing the spin-polarized transport endowed by topological surface states. An intrinsic surface dominant transport is established when cooling the sample to low temperature or reducing the conduction channel length, both achieved in situ in the transport measurements with a four-probe scanning tunneling microscope without the need of further tailoring the sample. The topological surface states show characteristic transport behaviors with mobility about an order of magnitude higher than reported before, and a spin polarization approaching the theoretically predicted value. Our result demonstrates accessibility to the intrinsic high mobility spin transport of topological surface states, which paves a way to realizing topological spintronic devices.

3D Imaging and Manipulation of Subsurface Selenium Vacancies in PdSe_{2}.

Two-dimensional materials such as layered transition-metal dichalcogenides (TMDs) are ideal platforms for studying defect behaviors, an essential step towards defect engineering for novel material functions. Here, we image the 3D lattice locations of selenium-vacancy V_{Se} defects and manipulate them using a scanning tunneling microscope (STM) near the surface of PdSe_{2}, a recently discovered pentagonal layered TMD. The V_{Se} show a characterisitc charging ring in a spatially resolved conductance map, based on which we can determine its subsurface lattice location precisely. Using the STM tip, not only can we reversibly switch the defect states between charge neutral and charge negative, but also trigger migrations of V_{Se} defects. This allows a demonstration of direct "writing" and "erasing" of atomic defects and tracing the diffusion pathways. First-principles calculations reveal a small diffusion barrier of V_{Se} in PdSe_{2}, which is much lower than S vacancy in MoS_{2} or an O vacancy in TiO_{2}. This finding opens an opportunity of defect engineering in PdSe_{2} for such as controlled phase transformations and resistive-switching memory device application.

Surface Magnetism of Cobalt Nanoislands Controlled by Atomic Hydrogen.

Controlling the spin states of the surface and interface is key to spintronic applications of magnetic materials. Here, we report the evolution of surface magnetism of Co nanoislands on Cu(111) upon hydrogen adsorption and desorption with the hope of realizing reversible control of spin-dependent tunneling. Spin-polarized scanning tunneling microscopy reveals three types of hydrogen-induced surface superstructures, 1H-(2 × 2), 2H-(2 × 2), and 6H-(3 × 3), with increasing H coverage. The prominent magnetic surface states of Co, while being preserved at low H coverage, become suppressed as the H coverage level increases, which can then be recovered by H desorption. First-principles calculations reveal the origin of the observed magnetic surface states by capturing the asymmetry between the spin-polarized surface states and identify the role of hydrogen in controlling the magnetic states. Our study offers new insights into the chemical control of magnetism in low-dimensional systems.

Seamless Staircase Electrical Contact to Semiconducting Graphene Nanoribbons.

Electrical contact to low-dimensional (low-D) materials is a key to their electronic applications. Traditional metal contacts to low-D semiconductors typically create gap states that can pin the Fermi level (EF). However, low-D metals possessing a limited density of states at EF can enable gate-tunable work functions and contact barriers. Moreover, a seamless contact with native bonds at the interface, without localized interfacial states, can serve as an optimal electrode. To realize such a seamless contact, one needs to develop atomically precise heterojunctions from the atom up. Here, we demonstrate an all-carbon staircase contact to ultranarrow armchair graphene nanoribbons (aGNRs). The coherent heterostructures of width-variable aGNRs, consisting of 7, 14, 21, and up to 56 carbon atoms across the width, are synthesized by a surface-assisted self-assembly process with a single molecular precursor. The aGNRs exhibit characteristic vibrational modes in Raman spectroscopy. A combined scanning tunneling microscopy and density functional theory study reveals the native covalent-bond nature and quasi-metallic contact characteristics of the interfaces. Our electronic measurements of such seamless GNR staircase constitute a promising first step toward making low resistance contacts.

Identification of a long non-coding RNA-associated RNP complex regulating metastasis at the translational step.

Long non-coding RNAs (lncRNAs) are a novel class of regulatory genes that play critical roles in various processes ranging from normal development to human diseases such as cancer progression. Recent studies have shown that lncRNAs regulate the gene expression by chromatin remodelling, transcription, splicing and RNA decay control, enhancer function, and epigenetic regulation. However, little is known about translation regulation by lncRNAs. We identified a translational regulatory lncRNA (treRNA) through genome-wide computational analysis. We found that treRNA is upregulated in paired clinical breast cancer primary and lymph-node metastasis samples, and that its expression stimulates tumour invasion in vitro and metastasis in vivo. Interestingly, we found that treRNA downregulates the expression of the epithelial marker E-cadherin by suppressing the translation of its mRNA. We identified a novel ribonucleoprotein (RNP) complex, consisting of RNA-binding proteins (hnRNP K, FXR1, and FXR2), PUF60 and SF3B3, that is required for this treRNA functions. Translational suppression by treRNA is dependent on the 3'UTR of the E-cadherin mRNA. Taken together, our study indicates a novel mechanism of gene regulation by lncRNAs in cancer progression.