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Background Jagged ends of plasma DNA are a recently recognized class of fragmentomic markers for cell-free DNA, reflecting the activity of nucleases. A number of recent studies have also highlighted the importance of jagged ends in the context of pregnancy and oncology. However, knowledge regarding the generation of jagged ends is incomplete. Methods Jaggedness of plasma DNA was analyzed based on Jag-seq, which utilized the differential methylation signals introduced by the DNA end-repair process. We investigated the jagged ends in plasma DNA using mouse models by deleting the deoxyribonuclease 1 (Dnase1), DNA fragmentation factor subunit beta (Dffb), or deoxyribonuclease 1 like 3 (Dnase1l3) gene. Results Aberrations in the profile of plasma DNA jagged ends correlated with the type of nuclease that had been genetically deleted, depending on nucleosomal structures. The deletion of Dnase1l3 led to a significant reduction of jaggedness for those plasma DNA molecules involving more than 1 nucleosome (e.g., size ranges 240-290 bp, 330-380 bp, and 420-470 bp). However, less significant effects of Dnase1 and Dffb deletions were observed regarding different sizes of DNA fragments. Interestingly, the aberration in plasma DNA jagged ends related to multinucleosomes was observed in human subjects with familial systemic lupus erythematosus with Dnase1l3 deficiency and human subjects with sporadic systemic lupus erythematosus. Conclusions Detailed understanding of the relationship between nuclease and plasma DNA jaggedness has opened up avenues for biomarker development.

In this paper, the properties of two-dimensional (2D) gallium nitride (GaN) photocathodes with a uniform doping and variable doping structure are studied by using Mg as a doping element based on first principles. The stability, bandstructure, work function, density of state and optical properties of the GaN bilayer and GaN trilayer in two-doped ways are investigated. The results show that formation energy of variable doping structure is less than that of the uniform doping structure, which means that the variable doping structure is more stable. At the same time, the formation energy increases with increase of layers. The pristine GaN bilayer has an indirect bandgap, while the doped GaN bilayer transforms into a direct bandgap. The impurity levels appear in a forbidden band of doped GaN trilayers, which is favorable for electron transition. The results of work function reveal that variable doping structure has lower vacuum barriers and more electron escape numbers, which proves that it can improve the quantum efficiency of photocathodes. Finally, the analysis of optical properties shows that the uniform doping structure has better optical properties than that of the variable doping structure.

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of rice blight disease as well as a serious phytopathogen worldwide. It is also one of the model organisms for studying bacteria-plant interactions. Current progress in bacterial signal transduction pathways has identified cyclic di-GMP as a major second messenger molecule in controlling Xanthomonas pathogenicity. However, it still remains largely unclear how c-di-GMP regulates the secretion of bacterial virulence factors in Xoo. In this study, we focused on the important roles played by DgcA (XOO3988), one of our previously identified diguanylate cyclases in Xoo, through further investigating the phenotypes of several dgcA-related mutants, namely, the dgcA-knockout mutant ΔdgcA, the dgcA overexpression strain OdgcA, the dgcA complemented strain CdgcA and the wild-type strain. The results showed that dgcA negatively affected virulence, EPS production, bacterial autoaggregation and motility, but positively triggered biofilm formation via modulating the intracellular c-di-GMP levels. RNA-seq data further identified 349 differentially expressed genes controlled by DgcA, providing a foundation for a more solid understanding of the signal transduction pathways in Xoo. Collectively, the present study highlights DgcA as a major regulator of Xoo virulence and can serve as a potential target for preventing rice blight diseases.

Manganese(II) contamination is naturally occurring in many groundwater and surface water sources. Moreover, industrial wastewater is also responsible for much of the Mn(II) contamination. Nowadays, Mn(II) contamination has become a serious environmental problem in some regions of the world. To explore a biological approach for removing excessive amounts of aqueous Mn(II) from water, we found a new biocatalyst multicopper oxidase CueO, which was firstly proved to catalyze the oxidation of Mn(II) both in vitro and in vivo . Subsequently, we established a CueO-mediated catalysis system to prepare biogenic Mn oxide (BioMnO x ), which was confirmed to be γ-Mn 3 O 4 by X-ray diffraction. This newly prepared BioMnO x consisted of 53.6% Mn(II), 18.4% Mn(III) and 28.0% Mn(IV) characterized by X-ray photoelectron spectroscopy. It exhibited distinct polyhedral structure with nanoparticles of 150–350 nm diameters observed by transmission electron microscopy. Importantly, CueO could remove 35.7% of Mn(II) after a seven-day reaction, and on the other hand, the cueO -overexpressing Escherichia coli strain (ECueO) could also oxidize 58.1% dissolved Mn(II), and simultaneously remove 97.7% Mn(II). Based on these results, we suggest that ECueO strain and CueO enzyme have potential applications on Mn(II) decontamination in water treatment.