Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine.

Multiomics require concerted recording of independent information, ideally from a single experiment. In this study, we introduce RIMS-seq2, a high-throughput technique to simultaneously sequence genomes and overlay methylation information while requiring only a small modification of the experimental protocol for high-throughput DNA sequencing to include a controlled deamination step. Importantly, the rate of deamination of 5-methylcytosine is negligible and thus does not interfere with standard DNA sequencing and data processing. Thus, RIMS-seq2 libraries from whole- or targeted-genome sequencing show the same germline variation calling accuracy and sensitivity compared with standard DNA-seq. Additionally, regional methylation levels provide an accurate map of the human methylome.

Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment.

Covalent modifications of genomic DNA are crucial for most organisms to survive. Amplicon-based high-throughput sequencing technologies erase all DNA modifications to retain only sequence information for the four canonical nucleobases, necessitating specialized technologies for ascertaining epigenetic information. To also capture base modification information, we developed Methyl-SNP-seq, a technology that takes advantage of the complementarity of the double helix to extract the methylation and original sequence information from a single DNA molecule. More specifically, Methyl-SNP-seq uses bisulfite conversion of one of the strands to identify cytosine methylation while retaining the original four-bases sequence information on the other strand. As both strands are locked together to link the dual readouts on a single paired-end read, Methyl-SNP-seq allows detecting the methylation status of any DNA even without a reference genome. Because one of the strands retains the original four nucleotide composition, Methyl-SNP-seq can also be used in conjunction with standard sequence-specific probes for targeted enrichment and amplification. We show the usefulness of this technology in a broad spectrum of applications ranging from allele-specific methylation analysis in humans to identification of methyltransferase specificity in complex bacterial communities.

Ingenious Synergy of a Pathology-Specific Biomimetic Multifunctional Nanoplatform for Targeted Therapy in Rheumatoid Arthritis.

Based on the pathological characteristics of rheumatoid arthritis, including the overproduction of reactive oxygen species (ROS), inflammatory responses, and osteoclast differentiation, a biomimetic multifunctional nanomedicine (M-M@I) is designed. Iguratimod (IGU) is loaded, which inhibits inflammatory responses and osteoclast differentiation, into mesoporous polydopamine (MPDA), which scavenges ROS. Subsequently, the nanoparticles are coated with a cell membrane of macrophages to achieve actively targeted delivery of the nanoparticles to inflamed joints. It is shown that the M-M@I nanoparticles are taken up well by lipopolysaccharide-induced RAW 264.7 macrophages or bone marrow-derived macrophages (BMDMs). In vitro, the M-M@I nanoparticles effectively scavenge ROS, downregulate genes related to inflammation promotion and osteoclast differentiation, and reduce the proinflammatory cytokines and osteoclast-related enzymes. They also reduce the polarization of macrophages to a pro-inflammatory M1 phenotype and inhibit differentiation into osteoclasts. In mice with collagen-induced arthritis, the M-M@I nanoparticles accumulate at arthritic sites and circulate longer, significantly mitigating arthritis symptoms and bone destruction. These results suggest that the pathology-specific biomimetic multifunctional nanoparticles are effective against rheumatoid arthritis, and they validate the approach of developing multifunctional therapies that target various pathological processes simultaneously.

Computational markers of risky decision-making predict for relapse to alcohol.

BACKGROUND: Relapse remains the major challenge in treatment of alcohol use disorder (AUD). Aberrant decision-making has been found as important cognitive mechanism underlying relapse, but factors associated with relapse vulnerability are unclear. Here, we aim to identify potential computational markers of relapse vulnerability by investigating risky decision-making in individuals with AUD. METHODS: Forty-six healthy controls and fifty-two individuals with AUD were recruited for this study. The risk-taking propensity of these subjects was investigated using the balloon analog risk task (BART). After completion of clinical treatment, all individuals with AUD were followed up and divided into a non-relapse AUD group and a relapse AUD group according to their drinking status. RESULTS: The risk-taking propensity differed significantly among healthy controls, the non-relapse AUD group, and the relapse AUD group, and was negatively associated with the duration of abstinence in individuals with AUD. Logistic regression models showed that risk-taking propensity, as measured by the computational model, was a valid predictor of alcohol relapse, and higher risk-taking propensity was associated with greater risk of relapse to drink. CONCLUSION: Our study presents new insights into risk-taking measurement and identifies computational markers that provide prospective information for relapse to drink in individuals with AUD.

Safety and Efficacy of Stent-Graft in the Treatment of Aortoiliac Artery Occlusive Disease: A Multicenter Study of Short-Term and Medium-Term Outcomes.

BACKGROUND: To evaluate the short-term and mid-term safety and efficacy of stent-graft compared with bare stents for treatment of aortoiliac occlusive disease (AIOD). METHODS: One hundred eighty three patients diagnosed with AIOD who received stent implantation at 3 vascular centers in north China between January 2019 and December 2021 were enrolled. Patients were divided into those undergoing stent-graft (Group A; n = 67) or bare stent (Group B; n = 116) implantation for retrospective cohort analysis. Efficacy was assessed as surgical success rate and rate of freedom from clinically driven target lesion reintervention at each follow-up time point. Safety was assessed by the rate of perioperative complication, major limb amputation, and aortoiliac artery-related mortality. RESULTS: There were no preoperative baseline differences between the 2 groups (P > 0.05). The surgical success was 91.04% for Group A, significantly higher than that for Group B (79.31%; P < 0.05). Incidence of perioperative complications was 2.98% for Group A, significantly lower than that for Group B (9.48%, P < 0.05), as was the rate of major limb amputation (A: 1.49% vs. B: 5.17%) and aortoiliac artery-related mortality (A: 1.49% vs. B: 4.31%), although these 2 indicators were not significantly different (P > 0.05). Follow-up rates were 91.8% for the total follow-up time of 3 years. Kaplan-Meier survival curve analysis gave significantly higher 1-year and 2-year freedom from clinically driven target lesion reintervention for Group A (98.51% and 95.52%) than for Group B (95.69% and 89.66%, P < 0.05). CONCLUSIONS: Stent-graft is more effective and safer than bare stent in the treatment of AIOD.

An Interspecies Recombinant Sida Yellow Mosaic China Virus Isolate and Betasatellite Cause a Leaf Curl Disease in Tobacco in Hainan, China.

Tobacco (Nicotiana tabacum) is an herbaceous crop. Cigar tobacco, a group of tobacco cultivars, has recently been planted in a few provinces in China. Since its introduction, symptoms such as leaf curling and vein thickening have appeared. Here we report a begomovirus, Sida yellow mosaic China virus-Hainan isolate (designated SiYMCNV-HN), associated with the betasatellite (designated SiYMCNB-HN) as the causal agent of a leaf curl disease in cigar tobacco (N. tabacum cv. Haiyan101) in Hainan Province, China. Phylogenetic and recombination analyses indicate that SiYMCNV-HN is an interspecies recombinant with a SiYMCNV isolate as the major parent and a Sida yellow vein Vietnam virus isolate as the minor parent. Full-length infectious clones of SiYMCNV-HN and SiYMCNB-HN were generated, which were highly infectious and induced high pathogenicity through agroinfiltration in Nicotiana benthamiana and N. tabacum. This newly reported recombinant begomovirus poses potential threats to tobacco plantations in the region.

The Role of the Gut Microbiome in the Development of Acute Pancreatitis.

With the explosion research on the gut microbiome in the recent years, much insight has been accumulated in comprehending the crosstalk between the gut microbiota community and host health. Acute pancreatitis (AP) is one of the gastrointestinal diseases associated with significant morbidity and subsequent mortality. Studies have elucidated that gut microbiota are engaged in the pathological process of AP. Herein, we summarize the major roles of the gut microbiome in the development of AP. We then portray the association between dysbiosis of the gut microbiota and the severity of AP. Finally, we illustrate the promises and challenges that arise when seeking to incorporate the microbiome in acute pancreatitis treatment.

Cyclooctatetraene-Embedded Carbon Nanorings.

With the prosperity of the development of carbon nanorings, certain topologically or functionally unique units-embedded carbon nanorings have sprung up in the past decade. Herein, we report the facile and efficient synthesis of three cyclooctatetraene-embedded carbon nanorings (COTCNRs) that contain three (COTCNR1 and COTCNR2) and four (COTCNR3) COT units in a one-pot Yamamoto coupling. These nanorings feature hoop-shaped segments of Gyroid (G-), Diamond (D-), and Primitive (P-) type carbon schwarzites. The conformations of the trimeric nanorings COTCNR1 and COTCNR2 are shape-persistent, whereas the tetrameric COTCNR3 possesses a flexible carbon skeleton which undergoes conformational changes upon forming host-guest complexes with fullerenes (C60 and C70), whose co-crystals may potentially serve as fullerene-based semiconducting supramolecular wires with electrical conductivities on the order of 10-7 S cm-1 (for C60⊂COTCNR3) and 10-8 S cm-1 (for C70⊂COTCNR3) under ambient conditions. This research not only describes highly efficient one-step syntheses of three cyclooctatetraene-embedded carbon nanorings which feature hoop-shaped segments of distinctive topological carbon schwarzites, but also demonstrates the potential application in electronics of the one-dimensional fullerene arrays secured by COTCNR3.

Soluble and Processable Single-Crystalline Cationic Polymers.

Single-crystal-to-single-crystal (SCSC) polymerization offers an effective protocol for the environmentally friendly preparation of polymer single crystals (PSCs) with extremely high crystallinity and very large molecular weights. Single-crystal X-ray diffraction (SCXRD) serves as a powerful technique for the in-depth characterization of their structures at a molecular level. Hence, a fundamental understanding of the structure-property relationships of PSCs is within our reach. Most of the reported PSCs, however, suffer from poor solubility, a property which hampers their post-functionalization and solution processability when it comes to practical applications. Here, we report soluble and processable PSCs with rigid polycationic backbones by taking advantage of an ultraviolet-induced topochemical polymerization from an elaborately designed monomer that results in a multitude of photoinduced [2 + 2] cycloadditions. The high crystallinity and excellent solubility of the resulting polymeric crystals enable their characterization both in the solid state by X-ray crystallography and electron microscopy and in the solution phase by NMR spectroscopy. The topochemical polymerization follows first-order reaction kinetics to a first approximation. Post-functionalization of the PSCs by anion exchange renders them super-hydrophobic materials for water purification. Solution processability endows PSCs with excellent gel-like rheological properties. This research represents a major step towards the controlled synthesis and full characterization of soluble single-crystalline polymers, which may find application in the fabrication of PSCs with many different functions.

Red-light is an environmental effector for mutualism between begomovirus and its vector whitefly.

Environments such as light condition influence the spread of infectious diseases by affecting insect vector behavior. However, whether and how light affects the host defense which further affects insect preference and performance, remains unclear, nor has been demonstrated how pathogens co-adapt light condition to facilitate vector transmission. We previously showed that begomoviral ßC1 inhibits MYC2-mediated jasmonate signaling to establish plant-dependent mutualism with its insect vector. Here we show red-light as an environmental catalyzer to promote mutualism of whitefly-begomovirus by stabilizing ßC1, which interacts with PHYTOCHROME-INTERACTING FACTORS (PIFs) transcription factors. PIFs positively control plant defenses against whitefly by directly binding to the promoter of terpene synthase genes and promoting their transcription. Moreover, PIFs interact with MYC2 to integrate light and jasmonate signaling and regulate the transcription of terpene synthase genes. However, begomovirus encoded ßC1 inhibits PIFs' and MYC2' transcriptional activity via disturbing their dimerization, thereby impairing plant defenses against whitefly-transmitted begomoviruses. Our results thus describe how a viral pathogen hijacks host external and internal signaling to enhance the mutualistic relationship with its insect vector.