Besides the pandemic caused by the coronavirus outbreak, many other pathogenic microbes also pose a devastating threat to human health, for instance, pathogenic bacteria. Due to the lack of ...broad‐spectrum antibiotics, it is urgent to develop nonantibiotic strategies to fight bacteria. Herein, inspired by the localized “capture and killing” action of bacteriophages, a virus‐like peroxidase‐mimic (V‐POD‐M) is synthesized for efficient bacterial capture (mesoporous spiky structures) and synergistic catalytic sterilization (metal–organic‐framework‐derived catalytic core). Experimental and theoretical calculations show that the active compound, MoO3, can serve as a peroxo‐complex‐intermediate to reduce the free energy for catalyzing H2O2, which mainly benefits the generation of •OH radicals. The unique virus‐like spikes endow the V‐POD‐M with fast bacterial capture and killing abilities (nearly 100% at 16 µg mL–1). Furthermore, the in vivo experiments show that V‐POD‐M possesses similar disinfection treatment and wound skin recovery efficiencies to vancomycin. It is suggested that this inexpensive, durable, and highly reactive oxygen species (ROS) catalytic active V‐POD‐M provides a promising broad‐spectrum therapy for nonantibiotic disinfection.
A bioinspired, spiky, and highly catalytic‐active virus‐like peroxidase‐mimic (V‐POD‐M) is synthesized for the localized “capture and killing” eradication of pathogenic bacteria. Experimental and theoretical calculations demonstrate that the V‐POD‐M exhibits strong bacterial interactions and efficient capture, synergistic catalytic sterilization, and similar in vivo disinfection efficiency to that of vancomycin, which provides a promising broad‐spectrum therapy for nonantibiotic disinfection.
Abstract
Pathogenic drug-resistant bacteria represent a threat to human health, for instance, the methicillin-resistant
Staphylococcus aureus
(MRSA). There is an ever-growing need to develop ...non-antibiotic strategies to fight bacteria without triggering drug resistance. Here, we design a hedgehog artificial macrophage with atomic-catalytic centers to combat MRSA by mimicking the “capture and killing” process of macrophages. The experimental studies and theoretical calculations reveal that the synthesized materials can efficiently capture and kill MRSA by the hedgehog topography and substantial generation of •O
2
−
and HClO with its Fe
2
N
6
O catalytic centers. The synthesized artificial macrophage exhibits a low minimal inhibition concentration (8 μg/mL Fe-Art M with H
2
O
2
(100 μM)) to combat MRSA and rapidly promote the healing of bacteria-infected wounds on rabbit skin. We suggest that the application of this hedgehog artificial macrophage with “capture and killing” capability and high ROS-catalytic activity will open up a promising pathway to develop antibacterial materials for bionic and non-antibiotic disinfection strategies.
...the number of RNA-seq libraries from the plant community has been increasing exponentially in recent years (Figure 1a). Besides showing expression patterns from different tissues and developmental ...stages (Figure 1c–e), we also annotated the mutant-related groups and treatment-associated groups in our maize, rice, soybean, wheat and cotton database, respectively (Figure 1f,g). To reduce the quantification biases derived from differing bioinformatic processes, we processed the data of each species with a unified pipeline and the most up-to-date reference genomes (more details on the ‘Tutorials’ page and Appendix S1). ...the database also provided hyperlinks to check the expression level of the homologous genes in other plants and supported a built-in online Integrative Genomics Viewer (IGV) (Figure 1h; Robinson et al., 2017).
The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, ...we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length RNA profiling at a single-nucleus level in plants using isolated nuclei. Combined with 10x Genomics and Nanopore long-read sequencing, we validate the robustness of this approach in Arabidopsis root cells and the developing endosperm. Sequencing results demonstrate that it allows for uncovering alternative splicing and polyadenylation-related RNA isoform information at the single-cell level, which facilitates characterizing cell identities.
In plants, 22-nucleotide small RNAs trigger the production of secondary small interfering RNAs (siRNAs) and enhance silencing. DICER-LIKE2 (DCL2)-dependent 22-nucleotide siRNAs are rare in ...Arabidopsis (
) and are thought to function mainly during viral infection; by contrast, these siRNAs are abundant in many crops such as soybean (
) and maize (
). Here, we studied soybean 22-nucleotide siRNAs by applying CRISPR-Cas9 to simultaneously knock out the two copies of soybean
,
and
, in the Tianlong1 cultivar. Small RNA sequencing revealed that most 22-nucleotide siRNAs are derived from long inverted repeats (LIRs) and disappeared in the
double mutant. De novo assembly of a Tianlong1 reference genome and transcriptome profiling identified an intronic LIR formed by the chalcone synthase (CHS) genes
and
This LIR is the source of primary 22-nucleotide siRNAs that target other
genes and trigger the production of secondary 21-nucleotide siRNAs. Disruption of this process in
mutants substantially increased
mRNA levels in the seed coat, thus changing the coat color from yellow to brown. Our results demonstrated that endogenous LIR-derived transcripts in soybean are predominantly processed by GmDCL2 into 22-nucleotide siRNAs and uncovered a role for DCL2 in regulating natural traits.
Inspired by the idea of Ma et al. (Journal of the Franklin Institute, 2018), we adopt relaxation technique and introduce relaxation factors into the gradient based iterative (GI) algorithm, and the ...relaxed based iterative (RGI) algorithm is established to solve the generalized coupled complex conjugate and transpose Sylvester matrix equations. By applying the real representation and straighten operation, we contain the sufficient and necessary condition for convergence of the RGI method. In order to effectively utilize this algorithm, we further derive the optimal convergence parameter and some related conclusions. Moreover, to overcome the high dimension calculation problem, a sufficient condition for convergence with less computational complexity is determined. Finally, numerical examples are reported to demonstrate the availability and superiority of the constructed iterative algorithm.
In eukaryotes, genes are transcribed by RNA polymerase-II (Pol-II) and introns are removed by the spliceosome largely cotranscriptionally
; analysis using long-read sequencing revealed that splicing ...occurs immediately after Pol-II passes introns in yeast
. Here, we developed a Nanopore-based method to profile chromatin-bound RNA that enables the simultaneous detection of splicing status, Pol-II position and polyadenylation at the genome-wide scale in Arabidopsis. We found that more than half of the introns remain unspliced after Pol-II transcribes 1 kb past the 3' splice site, which is much slower than the rate of splicing reported in yeast
. Many of the full-length chromatin-bound RNA molecules are polyadenylated, yet still contain unspliced introns at specific positions. These introns are nearly absent in the cytoplasm and are resistant to nonsense-mediated decay, suggesting that they are post-transcriptionally spliced before the transcripts are released into the cytoplasm; we therefore termed these introns post-transcriptionally spliced introns (pts introns). Analysis of around 6,500 public RNA-sequencing libraries found that the splicing of pts introns requires the function of splicing-related proteins such as PRMT5 and SKIP, and is also influenced by various environmental signals. The majority of the intron retention events in Arabidopsis are at pts introns, suggesting that chromatin-tethered post-transcriptional splicing is a major contributor to the widespread intron retention that is observed in plants, and could be a mechanism to produce fully spliced functional mRNAs for rapid response.
The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods.
Here, we use single-molecule ...nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Arabidopsis and in atxrn3, fpa, and met1 mutants. Our data reveal a wide range of termination windows among genes, ranging from ~ 50 nt to over 1000 nt. We also observe efficient termination before downstream tRNA genes, suggesting that chromatin structure around the promoter region of tRNA genes may block pol II elongation. 5' Cleaved readthrough transcription in atxrn3 with delayed termination can run into downstream genes to produce normally spliced and polyadenylated mRNAs in the absence of their own transcription initiation. Consistent with previous reports, we also observe long chimeric transcripts with cryptic splicing in fpa mutant; but loss of CG DNA methylation has no obvious impact on termination in the met1 mutant.
Our method is applicable to establish a comprehensive termination landscape in a broad range of species.
By applying the weighted relaxation technique to the gradient-based iterative (GI) algorithm and taking proper weighted combinations of the solutions, this paper proposes the weighted, relaxed ...gradient-based iterative (WRGI) algorithm to solve the generalized coupled conjugate and transpose Sylvester matrix equations. With the real representation of a complex matrix as a tool, the necessary and sufficient conditions for the convergence of the WRGI algorithm are determined. Also, some sufficient convergence conditions of the WRGI algorithm are presented. Moreover, the optimal step size and the corresponding optimal convergence factor of the WRGI algorithm are given. Lastly, some numerical examples are provided to demonstrate the effectiveness, feasibility and superiority of the proposed algorithm.
In plants, RNA-directed DNA methylation （RdDM） plays an essential role in silencing transposable elements that would otherwise have a deleterious effect on genome integrity. RdDM is an important ...pathway that establishes and maintains de novo DNA methylation in all three sequence contexts： CG, CHG, and CHH （where H is A, C, or T）, and the methylation is targeted by 24-nt small interfering RNAs （siRNAs） （Law and Jacobsen, 2010）.
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