A universe of human gut-derived bacterial prophages: unveiling the hidden viral players in intestinal microecology

ABSTRACTProphages, which are an existing form of temperate phages that integrate into host genomes, have been found extensively present in diverse bacterial species. The human gut microbiome, characterized by its complexity, dynamism, and interconnectivity among multiple species, remains inadequately understood in terms of the global landscape of bacterial prophages. Here, we analyzed 43,942 human gut-derived bacterial genomes (439 species of 12 phyla) and identified 105,613 prophage regions in ~ 92% of them. 16254 complete prophages were distributed in ~ 24% of bacteria, indicating an extremely uneven prophage distribution across various species within the human gut. Among all identified prophages, ~4% possessed cross-genera (2–20 genera) integration capacity, while ~ 17% displayed broad infection host ranges (targeting 2–35 genera). Functional gene annotation revealed that antibiotic-resistance genes and toxin-related genes were detected in ~ 2.5% and ~ 5.8% of all prophages, respectively. Furthermore, through sequence alignments between our obtained prophages and publicly available human gut phageome contigs, we have observed that ~ 72% of non-redundant prophages are previously unreported genomes, and they illuminate ~ 6.5–9.5% of the individual intestinal “viral dark matter”. Our study represents the first comprehensive depiction of human gut-derived prophages, provides a substantial collection of reference sequences for forthcoming human gut phageome-related investigations, and potentially enables better risk assessment of prophage dissemination

Fluorine-Doped Cationic Carbon Dots for Efficient Gene Delivery

Carbon dots (CDs) focus great attention in a broad range of adhibitions because of their excellent optical properties and high biocompatibility and property adjustability. However, the developed CDs have rarely been used as effective gene vectors until now. In this work, we devised and synthesized novel fluorine-doped cationic CDs (FCDs) using tetrafluoroterephthalic acid as a fluorine source and using branched polyethylenimine to furnish positive charge sites. The FCDs achieve dramatic positive EGFP and luciferase gene transfection efficiency as well as low cytotoxicity in commonly used cell lines at a low weight ratio, even in primary and stem cells. It is worth pointing out that the FCDs possess superior efficiency and biocompatibility, compared to some widely used commercial reagents such as 25 kDa polyethylenimine and Lipofectamine 2000. In addition, the FCDs show excellent efficient transfection even at high serum concentration and low DNA dose, indicating potential practical applications

Large Emission Red-Shift of Carbon Dots by Fluorine Doping and Their Applications for Red Cell Imaging and Sensitive Intracellular Ag⁺ Detection

Heteroatom doping is one of the most effective routes to adjust the physicochemical and optical properties of carbon dots (CDs). However, fluorine (F) doped CDs have been barely achieved. In this work, a F-doping strategy was proposed and adopted to modulate optical properties of CDs. A kind of F-doped CDs was synthesized by a solvothermal process using aromatic F bearing moiety as the F source and shows much longer maximum emissions (up to 600 nm, red fluorescence) than that of undoped CDs, indicating a large emission red-shift effect by F-doping. In addition, the F-doped CDs have remarkable water-solubility, high biocompatibility, as well as excellent stability even under broad pH range, ionic strengths, and light illumination and thus can be used as a novel probe for the highly efficient cell imaging of various normal cells and cancer cells. The F-doped CDs can selectively bind to Ag⁺. It therefore makes the F-doped CDs be a highly sensitive probe for the detection of Ag⁺ under both aqueous solution and various biological systems. The huge potential of this F-doping strategy is indicated in the rational design of high-performance CDs, as well as in applications of clinical diagnosis and ion detection

Silk fibroin hydrogel adhesive enables sealed-tight reconstruction of meniscus tears

Despite orientationally variant tears of the meniscus, suture repair is the current clinical gold treatment. However, inaccessible tears in company with re-tears susceptibility remain unresolved. To extend meniscal repair tools from the perspective of adhesion and regeneration, we design a dual functional biologic-released bioadhesive (S-PIL10) comprised of methacrylated silk fibroin crosslinked with phenylboronic acid-ionic liquid loading with growth factor TGF-β1, which integrates chemo-mechanical restoration with inner meniscal regeneration. Supramolecular interactions of β-sheets and hydrogen bonds richened by phenylboronic acid-ionic liquid (PIL) result in enhanced wet adhesion, swelling resistance, and anti-fatigue capabilities, compared to neat silk fibroin gel. Besides, elimination of reactive oxygen species (ROS) by S-PIL10 further fortifies localized meniscus tear repair by affecting inflammatory microenvironment with dynamic borate ester bonds, and S-PIL10 continuously releases TGF-β1 for cell recruitment and bridging of defect edge. In vivo rabbit models functionally evidence the seamless and dense reconstruction of torn meniscus, verifying that the concept of meniscus adhesive is feasible and providing a promising revolutionary strategy for preclinical research to repair meniscus tears

Measurement Report : Wintertime new particle formation in the rural area of the North China Plain - influencing factors and possible formation mechanism

The high concentration of fine particles and gaseous pollutants makes polluted areas, such as the urban setting of North China Plain (NCP) of China, a different environment for new particle formation (NPF) compared to many clean regions. Such conditions also hold for other polluted environments in this region (for instance, the rural area of NCP), yet the underlying mechanisms for NPF remain less understood, owing to the limited observations of particles in the sub-3 nm range. Comprehensive measurements, particularly covering the particle number size distribution down to 1.3 nm, were conducted at a rural background site of Gucheng (GC) in the North China Plain (NCP) from 12 November to 24 December 2018. In total, five NPF events during the 39 effective days of measurements for the campaign were identified, with the mean particle nucleation rate (J(1.3)) and growth rate (GR(1.3-2.4)) being 22.0 cm(-3) s(-1) and 3.9 nm h(-1), respectively. During these 5 d, NPF concurrently occurred at an urban site in Beijing. Sharing similar sources and transport paths of air masses arriving at our site to that of urban Beijing, we hypothesize that NPF events during these days in this region might be a regional phenomenon. The simultaneous occurrence of NPF in both places implies that H2SO4-amine nucleation, concluded for urban Beijing there, could probably be the dominating mechanism for NPF at our rural site. The higher concentration of sulfuric acid during many non-event days compared to that of event days indicates that the content of sulfuric acid may not necessarily lead to NPF events under current atmosphere. Only when the condensation sink or coagulation sink was significantly lowered, atmospheric NPF occurred, implying that condensation sinks (CSs) and coagulation sinks (CoagSs) are the dominating factors controlling the occurrence of NPF for the present rural environment of the NCP, which is quite similar to the feature seen in urban Beijing.Peer reviewe

Probing the open ocean with the research sailing yacht Eugen Seibold for climate geochemistry

The 72-foot sailing yacht Eugen Seibold is a new research platform for contamination-free sampling of the water column and lowermost atmosphere for biological, chemical, and physical properties, and the exchange processes between the two realms. Operations started in 2019 in the Northeast Atlantic, and will focus on the tropical East Pacific from 2023 until 2025. Laboratories for air and seawater analyses are equipped with down-sized and automated state-of-the-art technology. Plankton nets and seawater samplers and probes are deployed over the custom-made A-frame at the stern of the boat. Near Real-Time Transfer (NRT) of underway data via satellite connection allows dynamic expedition planning to maximize gain of information. Data and samples are analyzed in collaboration with the international expert research community. Quality controlled data are published with the Data Publisher for Earth & Environmental Science PANGAEA. The entire suite of measurements is available for proxy calibration of planktic paleo-archives at high temporal and spatial resolution in relation to seawater and atmospheric parameters. The ultimate goal of the project is a better understanding of modern and past ocean and climate