Structural transitions upon guide RNA binding and their importance in Cas12g-mediated RNA cleavage.

Cas12g is an endonuclease belonging to the type V RNA-guided CRISPR-Cas family. It is known for its ability to cleave RNA substrates using a conserved endonuclease active site located in the RuvC domain. In this study, we determined the crystal structure of apo-Cas12g, the cryo-EM structure of the Cas12g-sgRNA binary complex and investigated conformational changes that occur during the transition from the apo state to the Cas12g-sgRNA binary complex. The conserved zinc finger motifs in Cas12g undergo an ordered-to-disordered transition from the apo to the sgRNA-bound state and their mutations negatively impact on target RNA cleavage. Moreover, we identified a lid motif in the RuvC domain that undergoes transformation from a helix to loop to regulate the access to the RuvC active site and subsequent cleavage of the RNA substrate. Overall, our study provides valuable insights into the mechanisms by which Cas12g recognizes sgRNA and the conformational changes it undergoes from sgRNA binding to the activation of the RNase active site, thereby laying a foundation for the potential repurposing of Cas12g as a tool for RNA-editing.

Structure of the Spring Viraemia of Carp Virus Ribonucleoprotein Complex Reveals Its Assembly Mechanism and Application in Antiviral Drug Screening.

Spring viremia of carp virus (SVCV) is a highly pathogenic Vesiculovirus infecting the common carp, yet neither a vaccine nor effective therapies are available to treat spring viremia of carp (SVC). Like all negative-sense viruses, SVCV contains an RNA genome that is encapsidated by the nucleoprotein (N) in the form of a ribonucleoprotein (RNP) complex, which serves as the template for viral replication and transcription. Here, the three-dimensional (3D) structure of SVCV RNP was resolved through cryo-electron microscopy (cryo-EM) at a resolution of 3.7 Å. RNP assembly was stabilized by N and C loops; RNA was wrapped in the groove between the N and C lobes with 9 nt nucleotide per protomer. Combined with mutational analysis, our results elucidated the mechanism of RNP formation. The RNA binding groove of SVCV N was used as a target for drug virtual screening, and it was found suramin had a good antiviral effect. This study provided insights into RNP assembly, and anti-SVCV drug screening was performed on the basis of this structure, providing a theoretical basis and efficient drug screening method for the prevention and treatment of SVC. IMPORTANCE Aquaculture accounts for about 70% of global aquatic products, and viral diseases severely harm the development of aquaculture industry. Spring viremia of carp virus (SVCV) is the pathogen causing highly contagious spring viremia of carp (SVC) disease in cyprinids, especially common carp (Cyprinus carpio), yet neither a vaccine nor effective therapies are available to treat this disease. In this study, we have elucidated the mechanism of SVCV ribonucleoprotein complex (RNP) formation by resolving the 3D structure of SVCV RNP and screened antiviral drugs based on the structure. It is found that suramin could competitively bind to the RNA binding groove and has good antiviral effects both in vivo and in vitro. Our study provides a template for rational drug discovery efforts to treat and prevent SVCV infections.

Comparative efficacy of different reconstruction methods after wide local excision of the nail unit: A retrospective study.

BACKGROUND: Wide local excision (WLE) of the nail unit is widely used in treating in situ and minimally invasive malignant subungual tumours. After WLE, diverse reconstruction methods have been reported. However, the best repair method has yet to be determined. OBJECTIVE: To compare the repair effects and postoperative morbidity of secondary intention healing (SIH), artificial dermis grafting combined with secondary intention healing (ADGSIH) and full-thickness skin grafting (FSG) after WLE of the nail unit. METHODS: We retrospectively reviewed 21 patients who underwent WLE of the nail unit. The re-epithelializing time, functional and cosmetic outcomes, postoperative complications and patients' satisfaction were assessed from the follow-up records. RESULTS: The FSG group showed more rapid healing and better functional and cosmetic outcomes than the SIH and ADGSIH groups. The ADGSIH and FSG groups showed significant pain relief compared to the SIH group. No serious early and late postoperative complications were reported. The median follow-up period was 26 months, and no recurrence was observed. All patients were satisfied with the treatment. CONCLUSIONS: FSG after the WLE of the nail unit is a therapeutic option with convenient application, significant pain relief, rapid recovery and satisfying functional and cosmetic outcomes.

Efficient Hot Electron Capture in CuPc/MoSe2 Heterostructure Assisted by Intersystem Crossing.

Efficient hot electron extraction is a promising approach to develop photovoltaic devices that exceed the Shockley-Queisser limit. However, experimental evidence of hot electron harvesting employing an organic-inorganic interface is still elusive. Here, we reveal the hot electron dynamics at a CuPc/MoSe2 interface using steady-state spectroscopy and transient absorption spectroscopy. A hot electron transfer efficiency of greater than 78% from MoSe2 to CuPc is observed, comparable to that achieved in quantum dot hybrid systems. The mechanism is proposed as follows: the photogenerated hot electrons in MoSe2 transfer to CuPc and form singlet charge transfer states, which subsequently transform into triplet charge transfer states assisted by the rapid intersystem crossing, inhibiting back-donation of electrons and facilitating exciton dissociation into CuPc polarons with a nanosecond lifetime. Our results demonstrate that the intersystem crossing of the hybrid electronic state at organic-inorganic interfaces may serve as a scheme to enable efficient hot electron extraction in photovoltaic devices.

Local Chiral Inversion of Thymine Dimers by Manipulating Single Water Molecules.

Water, as one of the most important and indispensable small molecules in vivo, plays a crucial role in driving biological self-assembly processes. Real-space detection and identification of water-induced organic structures and further capture of dynamic dehydration processes are important yet challenging, which would help to reveal the cooperation and competition mechanisms among water-involved noncovalent interactions. Herein, introduction of water molecules onto the self-assembled thymine (T) structures under ultrahigh vacuum (UHV) conditions results in the hydration of hydrogen-bonded T dimers forming a well-ordered water-involved T structure. Reversibly, a local dehydration process is achieved by in situ scanning tunneling microscopy (STM) manipulation on single water molecules, where the adjacent T dimers connected with water molecules undergo a local chiral inversion process with the hydrogen-bonding configuration preserved. Such a strategy enables real-space identification and detection of the interactions between water and organic molecules, which may also shed light on the understanding of biologically relevant self-assembly processes driven by water.

The effect of dermoscopy in assisting on defining surgical margins of basal cell carcinoma.

To investigate the diagnostic value of dermoscopy in defining the tumor margin of basal cell carcinoma (BCC) for the appropriate surgical margin. A total of 107 BCC patients were enrolled for this study. The tumor boundaries were observed by naked eye and dermoscope respectively, and 5 mm outward was used as surgical margin according to the dermoscopy-defined margin. Pathological examinations were performed at 2 mm intervals in the direction previously marked and the effect was assessed accordingly. There were still 16.8% of patients whose visual margin was insufficient to the dermoscopy-detected margin. With 2 mm excision margin from the dermoscopy-guided tumor margin, excision range in 12 patients (11.2%) proved to be inadequate, but only 18 surgical margins (4.2%) in the whole 428 excision margin specimens proved to be tumor-positive. While with 4 mm margin, residual lesion was observed in 2 (0.5%) of 107 BCC patients, and positive margin was found in 2 (0.3%) of 428 margin specimen. There has been no recurrence in our study so far. Dermoscopy is superior to visual inspection for defining BCC tumor margin. Under preoperative dermoscopy detection, a 4 mm excision margin of BCC can achieve a radical resection rate of 98.1%, and 92.3% for a 2 mm excision margin of pigmented BCC.

The State-of-the-Art Sensing Techniques in Human Activity Recognition: A Survey.

Human activity recognition (HAR) has become an intensive research topic in the past decade because of the pervasive user scenarios and the overwhelming development of advanced algorithms and novel sensing approaches. Previous HAR-related sensing surveys were primarily focused on either a specific branch such as wearable sensing and video-based sensing or a full-stack presentation of both sensing and data processing techniques, resulting in weak focus on HAR-related sensing techniques. This work tries to present a thorough, in-depth survey on the state-of-the-art sensing modalities in HAR tasks to supply a solid understanding of the variant sensing principles for younger researchers of the community. First, we categorized the HAR-related sensing modalities into five classes: mechanical kinematic sensing, field-based sensing, wave-based sensing, physiological sensing, and hybrid/others. Specific sensing modalities are then presented in each category, and a thorough description of the sensing tricks and the latest related works were given. We also discussed the strengths and weaknesses of each modality across the categorization so that newcomers could have a better overview of the characteristics of each sensing modality for HAR tasks and choose the proper approaches for their specific application. Finally, we summarized the presented sensing techniques with a comparison concerning selected performance metrics and proposed a few outlooks on the future sensing techniques used for HAR tasks.

A Novel Strategy for Identifying NSCLC MicroRNA Biomarkers and Their Mechanism Analysis Based on a Brand-New CeRNA-Hub-FFL Network.

Finding reliable miRNA markers and revealing their potential mechanisms will play an important role in the diagnosis and treatment of NSCLC. Most existing computational methods for identifying miRNA biomarkers only consider the expression variation of miRNAs or rely heavily on training sets. These deficiencies lead to high false-positive rates. The independent regulatory model is an important complement to traditional models of co-regulation and is more impervious to the dataset. In addition, previous studies of miRNA mechanisms in the development of non-small cell lung cancer (NSCLC) have mostly focused on the post-transcriptional level and did not distinguish between NSCLC subtypes. For the above problems, we improved mainly in two areas: miRNA identification based on both the NOG network and biological functions of miRNA target genes; and the construction of a 4-node directed competitive regulatory network to illustrate the mechanisms. NSCLC was classified as lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) in this work. One miRNA biomarker of LUAD (miR-708-5p) and four of LUSC (miR-183-5p, miR-140-5p, miR-766-5p, and miR-766-3p) were obtained. They were validated using literature and external datasets. The ceRNA-hub-FFL involving transcription factors (TFs), microRNAs (miRNAs), mRNAs, and long non-coding RNAs (lncRNAs) was constructed. There were multiple interactions among these components within the net at the transcriptional, post-transcriptional, and protein levels. New regulations were revealed by the network. Meanwhile, the network revealed the reasons for the previous conflicting conclusions on the roles of CD44, ACTB, and ITGB1 in NSCLC, and demonstrated the necessity of typing studies on NSCLC. The novel miRNA markers screening method and the 4-node directed competitive ceRNA-hub-FFL network constructed in this work can provide new ideas for screening tumor markers and understanding tumor development mechanisms in depth.

On-Surface Synthesis of [3]Radialenes via [1+1+1] Cycloaddition.

[3]Radialenes are the smallest carbocyclic structures with unusual topologies and cross-conjugated π-electronic structures. Here, we report a novel [1+1+1] cycloaddition reaction for the synthesis of aza[3]radialenes on the Ag(111) surface, where the steric hindrance of the chlorine substituents guides the selective and orientational assembling of the isocyanide precursors. By combining scanning tunneling microscopy, non-contact atomic force microscopy, and time-of-flight secondary ion mass spectrometry, we determined the atomic structure of the produced aza[3]radialenes. Furthermore, two reaction pathways including synergistic and stepwise are proposed based on density functional theory calculations, which reveal the role of the chlorine substituents in the activation of the isocyano groups via electrostatic interaction.

Ladder Phenylenes Synthesized on Au(111) Surface via Selective [2+2] Cycloaddition.

Ladder phenylenes (LPs) composed of alternating fused benzene and cyclobutadiene rings have been synthesized in solution with a maximum length no longer than five units. Longer polymeric LPs have not been obtained so far because of their poor stability and insolubility. Here, we report the synthesis of linear LP chains on the Au(111) surface via dehalogenative [2+2] cycloaddition, in which the steric hindrance of the methyl groups in the 1,2,4,5-tetrabromo-3,6-dimethylbenzene precursor improves the chemoselectivity as well as the orientation orderliness. By combining scanning tunneling microscopy and noncontact atomic force microscopy, we determined the atomic structure and the electronic properties of the LP chains on the metallic substrate and NaCl/Au(111). The tunneling spectroscopy measurements revealed the charged state of chains on the NaCl layer, and this finding is supported by density functional theory calculations, which predict an indirect bandgap and antiferromagnetism in the polymeric LP chains.

Possible Involvement of the IL-6/JAK2/STAT3 Pathway in the Hypothalamus in Depressive-Like Behavior of Rats Exposed to Chronic Mild Stress.

INTRODUCTION: The interleukin-6/janus kinase 2/signal transducer and activator of transcription 3 (IL-6/JAK2/STAT3) pathway plays an important role in immune function, but little research has focused on this pathway in depression. We sought to examine the relationship between the IL-6/JAK2/STAT3 pathway and depressive-like behavior. METHODS: Using a chronic mild stress (CMS) paradigm, a total of 36 adult male Sprague-Dawley rats were divided into four matched groups: (1) control + vehicle, (2) CMS + vehicle, (3) control + paroxetine, and (4) CMS + paroxetine. We investigated the effects of CMS on depressive-like behavior by using the forced swimming test (FST). Subsequently, the mRNA levels of members of the IL-6/JAK2/STAT3 pathway were assessed by qRT-PCR. RESULTS: We found that rats exposed to CMS displayed a significant increase in immobility time and a decrease in climbing time in the FST. Moreover, mRNA levels of IL-6, JAK2, and STAT3 in the hypothalamus were increased following CMS. We also found that mRNA levels of IL-6, JAK2, and STAT3 were normalized by paroxetine administration, which coincided with normalization of the depressive-like behavior. CONCLUSIONS: The IL-6/JAK2/STAT3 pathway may be activated in depression, and targeting this pathway may provide a novel effective therapeutic approach for the treatment of depression.

Bond-Scission-Induced Structural Transformation from Cumulene to Diyne Moiety and Formation of Semiconducting Organometallic Polyyne.

The structural transformation from symmetric cumulene to broken-symmetry polyyne within a one-dimensional (1-D) atomic carbon chain is a signature of Peierls distortion. Direct observation of such a structural transformation with single-bond resolution is, however, still challenging. Herein, we design a molecule with a cumulene moiety (Br2C═C═C═CBr2) and employ STM tip manipulation to achieve the molecular skeleton rearrangement from a cumulene to a diyne moiety (Br-C≡C-C≡C-Br). Furthermore, by an on-surface reaction strategy, thermally induced entire debromination (:C═C═C═C:) leads to the formation of a 1-D organometallic polyyne (-C≡C-C≡C-Au-) with a semiconducting characteristic, which implies that a Peierls-like transition may occur in a rationally designed molecular system with limited length.

Infectious hematopoietic necrosis virus N protein suppresses fish IFN1 production by targeting the MITA.

Interferon (IFN) is a vital antiviral factor in host in the early stages after the viral invasion. Meanwhile, viruses have to survive by taking advantage of the cellular machinery and complete their replication. As a result, viruses evolved several immune escape mechanisms to inhibit host IFN expression. However, the mechanisms used to escape the host's IFN system are still unclear for infectious hematopoietic necrosis virus (IHNV). In this study, we report that the N protein of IHNV inhibits IFN1 production in rainbow trout by degrading the MITA. Firstly, the upregulation of IFN1 promoter activity stimulated by poly I:C was suppressed by IHNV infection. Consistent with this result, the overexpression of the N protein of IHNV blocked the IFN1 transcription that was activated by poly I:C and MITA. Secondly, MITA was remarkably decreased by the overexpression of N protein at the protein level. Further analysis demonstrated that the N protein targeted MITA and promoted the ubiquitination of MITA. Taken together, these data suggested that the production of rainbow trout IFN1 could be suppressed by the N protein of IHNV via degrading MITA.

Transcriptome analysis reveals the molecular mechanism of hepatic fat metabolism disorder caused by Muscovy duck reovirus infection.

The aim of this work was to clarify the molecular mechanism underlying the fatty degeneration of livers infected with Muscovy duck reovirus (MDRV), which produces obvious white necrotic foci in the liver. Transcriptome data for MDRV-infected Muscovy duck livers and control livers were sequenced, assembled, and annotated with Illumina® HiSeq 2000. The differentially expressed genes were screened and their functions were analysed. We also determined and confirmed the molecular mechanism of the hepatic fat metabolism disorder caused by MDRV infection. The expression of 4190 genes was higher in the infected livers than in the control livers, and the expression of 1113 genes was reduced. A Gene Ontology analysis showed that these genes were involved in 48 biological functions, and were significantly enriched in 237 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The free fatty acid content was significantly higher in the livers of infected Muscovy ducks than in the control livers (P < 0.01). The KEGG analysis showed that MDRV infection inhibited the cholesterol efflux from hepatic cells and reduced the expression of key enzymes involved in fatty acid degradation (scavenger receptor class b type 1, ABCG8, and APOA4), leading to the accumulation of fatty acids and cholesterol in the liver cells. In this study, we have identified the genes differentially expressed in livers infected by MDRV, from which we inferred the genes associated with lipodystrophia, and elucidated the molecular mechanism of the hepatic steatosis induced by MDRV. ABBREVIATIONS: ABC: ATP binding cassette transport; ACADVL: acyl-CoA dehydrogenase, very long chain; ACAT: mitochondrial-like acetyl-CoA acetyltransferase A; ACAT2: acetyl-CoA acyltransferase 2; ACNAT2: acyl-coenzyme A amino acid N-acyltransferase 2-like; ACOT1: acyl-CoA thioesterase 1; ACOT7: acyl-CoA thioesterase 7; ACOX1: acyl-CoA oxidase 1, palmitoyl; ACSBG2: acyl-CoA synthetase bubblegum family member 2; ACSL1: acyl-CoA synthetase long-chain family member 1; ADH1: alcohol dehydrogenase 1; APOA4: apolipoprotein A-IV; ARV: avian reovirus; cDNA: complementary deoxyribonucleic acid; COG: Clusters of Orthologous Groups; DEG: differentially expressed gene; DGAT: diacylgycerol acyltransferase; DNA: deoxyribonucleic acid; ECI2: enoyl-CoA delta isomerase 2; EHHADH: enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase; FDR: false discovery rate; GCDH: Pseudopodoces humilis glutaryl-CoA dehydrogenase; GO: Gene Ontology; HADHA: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit; I-FABP: intestinal fatty acid binding protein; KEGG: Kyoto Encyclopedia of Genes and Genomes; L-FABP: liver fatty acid binding protein; MDRV: Muscovy duck reovirus; MOI: multiplicity of infection; NPC1L1: Niemann-Pick C1-like 1; qPCR: real-time quantitative polymerase chain reaction; RNA: ribonucleic acid; RNase: ribonuclease; RNA-seq: RNA sequencing technology; RPKM: reads per kilobase per million mapped reads; SR-B1: scavenger receptor class b type 1.

Direct Formation of C-C Triple-Bonded Structural Motifs by On-Surface Dehalogenative Homocouplings of Tribromomethyl-Substituted Arenes.

On-surface synthesis shows significant potential in constructing novel nanostructures/nanomaterials, which has been intensely studied in recent years. The formation of acetylenic scaffolds provides an important route to the fabrication of emerging carbon nanostructures, including carbyne, graphyne, and graphdiyne, which feature chemically vulnerable sp-hybridized carbon atoms. Herein, we designed and synthesized a tribromomethyl-substituted compound. By using a combination of high-resolution scanning tunneling microscopy, non-contact atomic force microscopy, and density functional theory calculations, we demonstrated that it is feasible to convert these compounds directly into C-C triple-bonded structural motifs by on-surface dehalogenative homocoupling reactions. Concurrently, sp3 -hybridized carbon atoms are converted into sp-hybridized ones, that is, an alkyl group is transformed into an alkynyl moiety. Moreover, we achieved the formation of dimer structures, one-dimensional molecular wires, and two-dimensional molecular networks on Au(111) surfaces, which should inspire further studies towards two-dimensional graphyne structures.

Unique Transformation from Graphene to Carbide on Re(0001) Induced by Strong Carbon-Metal Interaction.

During graphene growth on various transition metals in the periodic table, metal carbides always emerge to behave as complex intermediates. On VIII metals, metastable carbides usually evolve and then transform into graphene along the phase interfaces, and even no metal carbides can form on IB-IIB metals. In contrast, during graphene growth on group IVB-VIB metals, carbides are usually generated even before the evolution of graphene and stably exist throughout the whole growth process. However, for the remaining transition metals, e.g., group VIIB, located in between IVB-VIB and VIII, the interplay between graphene and carbide is still vague. Herein, on Re(0001) (VIIB), we have revealed a novel transition from graphene to metal carbide (reverse to that on VIII metals) for the first time. This transition experienced graphene decomposition, dissolution, and carbon segregation processes, as evidenced by scanning tunneling microscopy (STM) and on-site, variable-temperature low electron energy diffraction (LEED) characterizations. This work thus completes the picture about the interplay between graphene and carbide on/in transition metals in the periodic table, as well as discloses a new territory for the growth of carbon-related materials, especially the metal carbide.

Temperature-Triggered Sulfur Vacancy Evolution in Monolayer MoS2 /Graphene Heterostructures.

The existence of defects in 2D semiconductors has been predicted to generate unique physical properties and markedly influence their electronic and optoelectronic properties. In this work, it is found that the monolayer MoS2 prepared by chemical vapor deposition is nearly defect-free after annealing under ultrahigh vacuum conditions at ≈400 K, as evidenced by scanning tunneling microscopy observations. However, after thermal annealing process at ≈900 K, the existence of dominant single sulfur vacancies and relatively rare vacancy chains (2S, 3S, and 4S) is convinced in monolayer MoS2 as-grown on Au foils. Of particular significance is the revelation that the versatile vacancies can modulate the band structure of the monolayer MoS2 , leading to a decrease of the bandgap and an obvious n-doping effect. These results are confirmed by scanning tunneling spectroscopy data as well as first-principles theoretical simulations of the related morphologies and the electronic properties of the various defect types. Briefly, this work should pave a novel route for defect engineering and hence the electronic property modulation of three-atom-thin 2D layered semiconductors.

Hexagonal Boron Nitride-Graphene Heterostructures: Synthesis and Interfacial Properties.

Research on in-plane and vertically-stacked heterostructures of graphene and hexagonal boron nitride (h-BN) have attracted intense attentions for energy band engineering and device performance optimization of graphene. In this review article, recent advances in the controlled syntheses, interfacial structures, and electronic properties, as well as novel device constructions of h-BN and graphene heterostructures are highlighted. Firstly, diverse synthesis approaches for in-plane h-BN and graphene (h-BN-G) heterostructures are reviewed, and their applications in nanoelectronics are briefly introduced. Moreover, the interfacial structures and electronic properties of h-BN-G heterojunctions are discussed, and a zigzag type interface is found to preferentially evolve at the linking edge of the two structural analogues. Secondly, several synthetic routes for the vertically-stacked graphene/h-BN (G/h-BN) heterostructures are also reviewed. The role of h-BN as perfect dielectric layers in promoting the device performance of graphene is presented. Finally, future research directions in the synthesis and application of such heterostructures are discussed.

Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111).

Grain boundaries (GBs) of hexagonal boron nitride (h-BN) grown on Cu(111) were investigated by scanning tunneling microscopy/spectroscopy (STM/STS). The first experimental evidence of the GBs composed of square-octagon pairs (4|8 GBs) was given, together with those containing pentagon-heptagon pairs (5|7 GBs). Two types of GBs were found to exhibit significantly different electronic properties, where the band gap of the 5|7 GB was dramatically decreased as compared with that of the 4|8 GB, consistent with our obtained result from density functional theory (DFT) calculations. Moreover, the present work may provide a possibility of tuning the inert electronic property of h-BN via grain boundary engineering.

Glyceraldehyde-3-phosphate dehydrogenase is activated by lysine 254 acetylation in response to glucose signal.

The altered metabolism in most tumor cells consists of elevated glucose uptake and increased glycolysis even in the presence of high oxygen tension. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an obligatory enzyme in glycolysis. Here, we report that acetylation at lysine 254 (K254) increases GAPDH activity in response to glucose. Furthermore, acetylation of GAPDH (K254) is reversibly regulated by the acetyltransferase PCAF and the deacetylase HDAC5. Substitution of K254 to glutamine compromises the ability of GAPDH to support cell proliferation and tumor growth. Our study reveals a mechanism of GAPDH enzyme activity regulation by acetylation and its critical role in cellular regulation.