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Ribosomally synthesized and post-translationally modified peptides (RiPPs) are natural products with remarkable chemical and functional diversities. These peptides are often synthesized as signals or antibiotics and frequently associated with quorum sensing (QS) systems. With the increasing number of available genomes, many hitherto unseen RiPP biosynthetic pathways have been mined, providing new resources for novel bioactive compounds. Herein, we investigated the underexplored biosynthetic potential of Streptococci, prevalent bacteria in mammal–microbiomes that include pathogenic, mutualistic, and commensal members. Using the transcription factor-centric genome mining strategy, we discovered a new family of lanthipeptide biosynthetic loci under the control of potential QS. By in vitrostudies, we investigated the reaction of one of these lanthipeptide synthetases and found that it installs only one lanthionine moiety onto its short precursor peptide by connecting a conserved TxxC region. Bioinformatics and in vitrostudies revealed that these lanthipeptide synthetases (class VI) are novel lanthipeptide synthetases with a truncated lyase, a kinase, and a truncated cyclase domain. Our data provide important insights into the processing and evolution of lanthipeptide synthetase to tailor smaller substrates. The data are important for obtaining a mechanistic understanding of the post-translational biosynthesis machinery of the growing variety of lanthipeptides.

COVID‐19 is currently pandemic and the detection of SARS‐CoV‐2 variants in wastewater is causing widespread concern. Herein, cold atmospheric plasma (CAP) is proposed as a novel wastewater disinfection technology that effectively inactivates SARS‐CoV‐2 transcription‐ and replication‐competent virus‐like particles, coronavirus GX_P2V, pseudotyped SARS‐CoV‐2 variants, and porcine epidemic diarrhoea virus in a large volume of water within 180 s (inhibition rate > 99%). Further, CAP disinfection did not adversely affect the viability of various human cell lines. It is identified that CAP produced peroxynitrite (ONOO−), ozone (O3), superoxide anion radicals (O2−), and hydrogen peroxide (H2O2) as the major active substances for coronavirus disinfection. Investigation of the mechanism showed that active substances not only reacted with the coronavirus spike protein and affected its infectivity, but also destroyed the nucleocapsid protein and genome, thus affecting virus replication. This method provides an efficient and environmentally friendly strategy for the elimination of SARS‐CoV‐2 and other coronaviruses from wastewater. Cold atmospheric plasma can produce peroxynitrite (ONOO−), ozone (O3), superoxide anion radicals (O2−), and hydrogen peroxide (H2O2) as the major reactive species to inactivate coronaviruses by disrupting the viral Spike protein and genomic RNA, thus hindering viral entry and replication. This study highlights the potential of cold atmospheric plasma as a promising approach to combat coronavirus infections.

Ailanthus altissimais a deciduous tree native to China and introduced to other parts of the world as an ornamental plant. It exhibits resistance to both abiotic and biotic stress factors and has various pharmacological effects and strong allelopathy, generating significant research interests. However, the genome sequence of this species has not been reported, limiting its research development. The purpose of the study was to determine the genome size and characteristics of A. altissimato conduct its genomic survey. Next-generation sequencing and K-mer analysis were employed to measure the genome size of A. altissima. Overall, a total of 61.93 Gb high-quality clean data were acquired, representing approximately 64.09× coverage of the A. altissimagenome. The genomic characteristics of A. altissimainclude a genome size of 966.38 Mbp, a heterozygosis rate of 0.78 %, and a repeat rate of 41.22 %. A total of 735,179 genomic SSRs markers were identified based on genome survey sequences. Alignment analysis showed that A. altissimawas closely related to Citrus sinensisand Leitneria florida-na. This study provides basic information for future whole-genomic sequencing of A. altissima. This will facilitate a knowledge of the population structure, genetic diversity, long distance-gene transfer, and pollen-based gene flow analyses of A. altissimapopulations from its known distribution ranges in China, focusing on planted and natural forest stands.

Background: SMAD3 is a pivotal intracellular mediator for participating in the activation of multiple immune signal pathways. Objective: The epigenetic regulation mechanism of the positive immune factor SMAD3 in cervical cancer remains unknown. Therefore, the epigenetic regulation on SMAD3 is investigated in this study. Methods: The methylation status of SMAD3 was detected by Methylation-Specific PCR (MS-PCR) and Quantitative Methylation-Specific PCR (MS-qPCR) in cervical cancer tissues and cell lines. The underlying molecular mechanisms of SUV39H1-DNMT1-SMAD3 regulation were elucidated using cervical cancer cell lines containing siRNA or/and over-expression systems. The regulation of DNMT1 by SUV39H1 was confirmed using Chromatin Immunoprecipitation-qPCR (ChIP-qPCR). The statistical methods used for comparing samples between groups were paired t-tests and one-way ANOVAs. Results: H3K9me3 protein regulated by SUV39H1 directly interacts with the DNMT1 promoter region to regulate its expression in cervical cancer cells, resulting in the reduced expression of the downstream target gene DNMT1. In addition, DNMT1 mediates the epigenetic modulation of the SMAD3 gene by directly binding to its promoter region. The depletion of DNMT1 effectively restores the expression of SMAD3 in vitro. Moreover, in an in vivo assay, the expression profile of SUV39H1-DNMT1 was found to correlate with SMAD3 expression in accordance with the expression at the cellular level. Notably, the promoter region of SMAD3 was hypermethylated in cervical cancer tissues, and this hypermethylation inhibited the subsequent gene expression. Conclusion: These results indicate that SUV39H1-DNMT1 is a crucial SMAD3 regulatory axis in cervical cancer. SUV39H1-DNMT1 axis may provide a potential therapeutic target for the treatment of cervical cancer.

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ABSTRACTThe fully synthetic humanized phage antibody library has the advantages including the minimized immunogenicity, which frequently happened in hybridoma cell-based antibody production. In this paper, using the constructed diverse complementarity determining region gene library and the germline gene as the backbone, we constructed eight single-chain antibody libraries and a combinatorial antibody library with a big capacity of 1.41 × 1010. M13EEA helper phage that was engineered from M13KO7 was applied to prepare phage antibody library. The eukaryotic expression of T-cell immune receptor with Ig and ITIM domain (TIGIT) antigen was used as a target antigen for screening. The screening of antigen-specific single-chain Fc-fused protein was performed through evaluation of binding affinity based on ELISA analysis. The IgG antibody was prepared with the screened single-chain protein. Finally, the CB3 antibody was screened out which exhibits the highest binding affinity with TIGIT with the Kdvalue of 8.155 × 10−10 M.

Image segmentation is to partition one given image into different regions. In essence, the procedure of image segmentation is to cluster the pixels into different groups according to the retrieved features. However, artefacts in the given images make the features be contaminated, resulting in poor performance of current segmentation algorithms. Therefore, how to reduce the effect of image artefacts is one hot topic in image processing. In current algorithms, neighbour information is adopted to resist the effect of image artefacts. However, when the image is contaminated with high-level noise, current algorithms also perform poor. Recently, non-local information is introduced to improve the quality of segmentation results, in which pixel relevance between pixels is crucial. In this paper, pixel relevance is measured based on Mahalanobis distance. More specifically, we consider the distribution of different samples and relevance interference between samples in the procedure of computing pixel relevance. Then, a new algorithm based on the novel pixel relevance is proposed, where non-local information can be incorporated into fuzzy clustering for image segmentation. The new algorithm can improve the robustness of corresponding algorithms greatly. Experiments on different noisy images show that the proposed algorithm can retrieve better results than conventional algorithms.

Coal gangue was calcinated under air, nitrogen, carbon dioxide, air–hydrogen, and hydrogen atmospheres. The effects of different calcination temperatures and atmospheres on the mineral composition of activated coal gangue were investigated by X-ray diffraction. Moreover, the acid leaching kinetics of aluminum oxide from coal gangue was investigated with sulfuric acid. It showed that the air atmosphere promoted kaolinite decomposition during coal gangue calcination. The hydrogen atmosphere promoted the activation and decomposition of kaolinite at reaction temperatures exceeding 650°C. The carbon dioxide atmosphere eliminated the influence of residual carbon on coal gangue. When the ratio of acid/coal gangue was 1.5 and reaction temperature was 650°C, the sulfuric acid leaching rate under air, air-hydrogen, carbon dioxide, hydrogen and nitrogen atmospheres were 93.66%, 90.90%, 84.06%, 81.91% and 77.54% respectively. The acid leaching reaction process conformed to unreacted shrinking core model of particle unchanged, and was controlled by the interfacial chemical reaction. The reaction kinetic equation for the leaching process was 1-(1-x)1/3=kt with an apparent activation energy of 48.97 kJ/mol.

The geographical origin and radiation of holarctica-type tularemia, which has spread across the northern hemisphere, is open to scientific debate. Here, through phylogenetics, we show that five Tibetan Francisella tularensisisolates subsp. holarcticacluster between basal-positioned Japanese isolates and all other subspecies strains in the world, providing evidence for a previously unknown intermediate lineage next to the Japanese isolates. Importantly, identification of this new intermediate lineage complements current knowledge of tularemia epidemiology, supporting a geographical origin and radiation of the subsp. holarcticain Asia. In addition, thirteen Tibetan isolates belonging to a clade previously found only in North America and Scandinavia, further increases the diversity of holarcticastrains in Asia. In summary, this study provides evidence for an Asian origin and radiation of holarctica-type tularemia.

ABSTRACTChlamydia trachomatisis an obligate intracellular epitheliotropic bacterial pathogen of humans. Infection of the eye can result in trachoma, the leading cause of preventable blindness in the world. The pathophysiology of blinding trachoma is driven by multiple episodes of reinfection of conjunctival epithelial cells, producing an intense chronic inflammatory response resulting in submucosal tissue remodeling and scarring. Recent reports have shown that infection with trachoma organisms lacking the cryptic chlamydial plasmid is highly attenuated in macaque eyes, a relevant experimental model of human trachoma infection. To better understand the molecular basis of plasmid-mediated infection attenuation and the potential modulation of host immunity, we conducted transcriptional profiling of human epithelial cells infected with C. trachomatisplasmid-bearing (A2497) and plasmid-deficient (A2497P−) organisms. Infection of human epithelial cells with either strain increased the expression of host genes coding for proinflammatory (granulocyte-macrophage colony-stimulating factor [GM-CSF], macrophage colony-stimulating factor [MCSF], interleukin-6 [IL-6], IL-8, IL-1α, CXCL1, CXCL2, CXCL3, intercellular adhesion molecule 1 [ICAM1]), chemoattraction (CCL20, CCL5, CXCL10), immune suppression (PD-L1, NFKB1B, TNFAIP3, CGB), apoptosis (CASP9, FAS, IL-24), and cell growth and fibrosis (EGR1 and IL-20) proteins. Statistically significant increases in the levels of expression of many of these genes were found in A2497-infected cells compared to the levels of expression in A2497P−-infected cells. Our findings suggest that the chlamydial plasmid plays a focal role in the host cell inflammatory response to infection and immune avoidance. These results provide new insights into the role of the chlamydial plasmid as a chlamydial virulence factor and its contributions to trachoma pathogenesis.

Lasso peptides are unique natural products that comprise a class of ribosomally synthesized and post-translationally modified peptides. Their defining three-dimensional structure is a lariat knot, in which the C-terminal tail is threaded through a macrolactam ring formed between the N-terminal amino group and an Asp or Glu side chain (i.e., an isopeptide bond). Recent genome mining strategies have revealed various types of lasso peptide biosynthetic gene clusters and have thus redefined the known chemical space of lasso peptides. To date, over 20 different types of these gene clusters have been discovered, including several different clades from Proteobacteria. Despite the diverse architectures of these gene clusters, which may or may not encode various tailoring enzymes, most currently known lasso peptides are synthesized by two discrete clades defined by the presence of an ATP-binding cassette transporter or its absence and (sometimes) concurrent appearance of an isopeptidase, raising questions about their evolutionary history. Herein, we discovered and characterized the lasso peptide rubrinodin, which is assembled by a gene cluster encoding both an ATP-binding cassette transporter and an isopeptidase. Our bioinformatics analyses of this and other representative cluster types provided new clues into the evolutionary history of lasso peptides. Furthermore, our structural and biochemical investigations of rubrinodin permitted the conversion of this thermolabile lasso peptide into a more thermostable scaffold.

ABSTRACTChlamydia trachomatiscauses chronic inflammatory diseases of the eye and genital tract and has global medical importance. The chlamydial plasmid plays an important role in the pathophysiology of these diseases, as plasmid-deficient organisms are highly attenuated. The cryptic plasmid carries noncoding RNAs and eight conserved open reading frames (ORFs). To understand plasmid gene function, we generated plasmid shuttle vectors with deletions in each of the eight ORFs. The individual deletion mutants were used to transform chlamydiae and the transformants were characterized phenotypically and at the transcriptional level. We show that pgp1, -2, -6, and -8are essential for plasmid maintenance, while the other ORFs can be deleted and the plasmid stably maintained. We further show that a pgp4knockout mutant exhibits an in vitrophenotype similar to its isogenic plasmidless strain, in terms of abnormal inclusion morphology and lack of glycogen accumulation. Microarray and qRT-PCR analysis revealed that Pgp4 is a transcriptional regulator of plasmid-encoded pgp3and multiple chromosomal genes, including the glycogen synthase gene glgA, that are likely important in chlamydial virulence. Our findings have major implications for understanding the plasmid's role in chlamydial pathogenesis at the molecular level.

A novel [Ru(bpy)2(dcbpy)NHS] labeling/aptamer‐based biosensor combined with gold nanoparticle amplification for the determination of lysozyme with an electrochemiluminescence (ECL) method is presented. In this work, an aptamer, an ECL probe, gold nanoparticle amplification, and competition assay are the main protocols employed in ECL detection. With all the protocols used, an original biosensor coupled with an aptamer and [Ru(bpy)2(dcbpy)NHS] has been prepared. Its high selectivity and sensitivity are the main advantages over other traditional [Ru(bpy)3]2+biosensors. The electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM) characterization illustrate that this biosensor is fabricated successfully. Finally, the biosensor was applied to a displacement assay in different concentrations of lysozyme solution, and an ultrasensitive ECL signal was obtained. The ECL intensity decreased proportionally to the lysozyme concentration over the range 1.0×10−13–1.0×10−8mol L−1with a detection limit of 1.0×10−13mol L−1. This strategy for the aptasensor opens a rapid, selective, and sensitive route for the detection of lysozyme and potentially other proteins.

Two nitrilotriacetate cobalt complexes {[CoK2(NTA)(Hmta)(H2O)3]NO3}n(1) and [{Co(4,4′‐bpy)2(H2O)4}{Co2(NTA)2(4,4′‐bpy)(H2O)2}] (2) (NTA = nitrilotriacetate anion, Hmta = hexamethylenetetramine and 4,4′‐bpy = 4,4′‐bipyridine) were prepared and characterized by IR, elemental analysis and single crystal X‐ray diffraction study. The influence of the neutral ancillary ligands on the formation of the complexes with different structures in the Co‐NTA system was discussed. The coordination of NTA and Hmta to Co2+ions only resulted in the formation of mononuclear [Co(NTA)(Hmta)]−ions which are further connected by K+ions and water molecules to form a three‐dimensional network. The use of 4,4′‐bpy as ancillary ligand in 2led to the formation of separate mononuclear [Co(4,4′‐bpy)2(H2O)4]2+and dinuclear [Co2(NTA)2(4,4′‐bpy)(H2O)2]2−which are further connected by hydrogen bonds to form a supramolecular three‐dimensional network. In these cases it seems to suggest that the addition of neutral ancillary ligand into the Co‐NTA system leads to the formation of lower dimensional structures when the contribution of alkali ions to the structural dimensionality is neglected.

Objective To evaluate whether diabetic retinopathy can be reversed after aflibercept, based on improvements in diabetic macular edema, hard exudates (HEs) of the posterior pole, and retinal microaneurysms (MAs).Methods This was a single-center retrospective study of 30 patients (34 eyes) with severe non-proliferative diabetic retinopathy (NPDR) who were treated between August and October 2018. Best-corrected visual acuity (BCVA), central foveal thickness (CFT), area of HEs, and number of MAs were compared before and after treatment.Results The mean patient age was 61.4 ± 7.1 years; 14 patients (46.7%) were men. The mean number of injections per patient was 3.5 ± 0.5. The time between the last injection and the last follow-up was 82 days (range, 78–110 days). Six months after the first intravitreal injection, significant improvement was observed in BCVA (from 0.70 ± 0.18 to 0.42 ± 0.19 logMAR), CFT (from 377.17 ± 60.41 to 261.21 ± 31.50 µm), and number of MAs (from 182.2 ± 77.4 to 101.5 ± 59.6). Observations over 6 months after the first intravitreal injection showed a statistically significant reduction in the area of HEs (P = 0.007). No adverse events occurred during the treatment period.Conclusion Diabetic retinopathy might be partially reversed by aflibercept treatment, as indicated by BCVA, CFT, number of MAs, and area of HEs.

cGAS-STING signaling is essential for innate immunity. Its misregulation promotes cancer or autoimmune and autoinflammatory diseases, and it is imperative to identify effective lead compounds that specifically downregulate the pathway. We report here that astin C, a cyclopeptide isolated from the medicinal plant Aster tataricus, inhibits cGAS-STING signaling and the innate inflammatory responses triggered by cytosolic DNAs. Moreover, mice treated with astin C are more susceptible to HSV-1 infection. Consistently, astin C markedly attenuates the autoinflammatory responses in Trex1−/−BMDM cells and in Trex1−/−mouse autoimmune disease model. Mechanistically, astin C specifically blocks the recruitment of IRF3 onto the STING signalosome. Collectively, this study characterizes a STING-specific small-molecular inhibitor that may be applied for potentially manipulating the STING-mediated clinical diseases.

ABSTRACTChlamydia trachomatisis an obligate intracellular bacterium that is a globally important human pathogen. The chlamydial plasmid is an attenuating virulence factor, but the molecular basis for attenuation is not understood. Chlamydiae replicate within a membrane-bound vacuole termed an inclusion, where they undergo a biphasic developmental growth cycle and differentiate from noninfectious into infectious organisms. Late in the developmental cycle, the fragile chlamydia-laden inclusion retains its integrity by surrounding itself with scaffolds of host cytoskeletal proteins. The ability of chlamydiae to developmentally free themselves from this cytoskeleton network is a fundamental virulence trait of the pathogen. Here, we show that plasmidless chlamydiae are incapable of disrupting their cytoskeletal entrapment and remain intracellular as stable mature inclusions that support high numbers of infectious organisms. By using deletion mutants of the eight plasmid-carried genes (Δpgp1to Δpgp8), we show that Pgp4, a transcriptional regulator of multiple chromosomal genes, is required for exit. Exit of chlamydiae is dependent on protein synthesis and is inhibited by the compound C1, an inhibitor of the type III secretion system (T3S). Exit of plasmid-free and Δpgp4organisms, which failed to lyse infected cells, was rescued by latrunculin B, an inhibitor of actin polymerization. Our findings describe a genetic mechanism of chlamydial exit from host cells that is dependent on an unknown pgp4-regulated chromosomal T3S effector gene.IMPORTANCEChlamydia's obligate intracellular life style requires both entry into and exit from host cells. Virulence factors that function in exiting are unknown. The chlamydial inclusion is stabilized late in the infection cycle by F-actin. A prerequisite of chlamydial exit is its ability to disassemble actin from the inclusion. We show that chlamydial plasmid-free organisms, and also a plasmid gene protein 4 (pgp4) null mutant, do not disassociate actin from the inclusion and fail to exit cells. We further provide evidence that Pgp4-regulated exit is dependent on the chlamydial type III secretion system. This study is the first to define a genetic mechanism that functions in chlamydial lytic exit from host cells. The findings also have practical implications for understanding why plasmid-free chlamydiae are highly attenuated and have the ability to elicit robust protective immune responses.