Light-Up Aptameric Sensor of Serotonin for Point-of-Care Use.

Serotonin is a vital neurotransmitter for regulating organism functions, and its abnormal level indicates multiple diseases. Aptamer has emerged as an innovative tool for serotonin analysis very recently; however, the current aptameric sensing platform lacks design flexibility and portability. Here, we introduce a light-up aptameric sensor using designer DNA molecules with tunable affinity and dynamic response and achieve mobile phone-based detection for point-of-care use. We develop a type of allosteric DNA sensor through flanking the serotonin recognition domain with split fluorogenic sequences, where both linker lengths and split sites of the aptamer affect its function. In addition, we design a series of molecular constructs that contain nucleotide mutations and systematically investigate the structure folding and ligand binding of the aptameric molecules. The results show distinct effects of variant mutation sites on conformation change and sensing responses. Notably, the variable aptameric molecules allow affinity and dynamic response regulation, which are adaptable to diverse sensing applications that require different threshold levels. Furthermore, we demonstrate a simple surface-based assay that can use smartphone imaging to visualize results for diagnosis. In a portable and simple manner, highly sensitive and selective serotonin assay is achieved in different biofluids, with detection limits in the low nanomolar range. This study offers an alternative approach for serotonin assay using engineered aptameric molecular probes. We expect that the practical utility may make the method promising in resource-limited settings.

m6 A promotes planarian regeneration.

Regeneration is the regrowth of damaged tissues or organs, a vital process in response to damages from primitive organisms to higher mammals. Planarian possesses active whole-body regenerative capability owing to its vast reservoir of adult stem cells, neoblasts, providing an ideal model to delineate the underlying mechanisms for regeneration. RNA N6 -methyladenosine (m6 A) modification participates in many biological processes, including stem cell self-renewal and differentiation, in particular the regeneration of haematopoietic stem cells and axons. However, how m6 A controls regeneration at the whole-organism level remains largely unknown. Here, we demonstrate that the depletion of m6 A methyltransferase regulatory subunit wtap abolishes planarian regeneration, potentially through regulating genes related to cell-cell communication and cell cycle. Single-cell RNA-seq (scRNA-seq) analysis unveils that the wtap knockdown induces a unique type of neural progenitor-like cells (NP-like cells), characterized by specific expression of the cell-cell communication ligand grn. Intriguingly, the depletion of m6 A-modified transcripts grn, cdk9 or cdk7 partially rescues the defective regeneration of planarian caused by wtap knockdown. Overall, our study reveals an indispensable role of m6 A modification in regulating whole-organism regeneration.

scm6A-seq reveals single-cell landscapes of the dynamic m6A during oocyte maturation and early embryonic development.

N6-methyladenosine (m6A) has been demonstrated to regulate RNA metabolism and various biological processes, including gametogenesis and embryogenesis. However, the landscape and function of m6A at single cell resolution have not been extensively studied in mammalian oocytes or during pre-implantation. In this study, we developed a single-cell m6A sequencing (scm6A-seq) method to simultaneously profile the m6A methylome and transcriptome in single oocytes/blastomeres of cleavage-stage embryos. We found that m6A deficiency leads to aberrant RNA clearance and consequent low quality of Mettl3Gdf9 conditional knockout (cKO) oocytes. We further revealed that m6A regulates the translation and stability of modified RNAs in metaphase II (MII) oocytes and during oocyte-to-embryo transition, respectively. Moreover, we observed m6A-dependent asymmetries in the epi-transcriptome between the blastomeres of two-cell embryo. scm6A-seq thus allows in-depth investigation into m6A characteristics and functions, and the findings provide invaluable single-cell resolution resources for delineating the underlying mechanism for gametogenesis and early embryonic development.

Djhsp60 Is Required for Planarian Regeneration and Homeostasis.

HSP60, a well-known mitochondrial chaperone, is essential for mitochondrial homeostasis. HSP60 deficiency causes dysfunction of the mitochondria and is lethal to animal survival. Here, we used freshwater planarian as a model system to investigate and uncover the roles of HSP60 in tissue regeneration and homeostasis. HSP60 protein is present in all types of cells in planarians, but it is relatively rich in stem cells and head neural cells. Knockdown of HSP60 by RNAi causes head regression and the loss of regenerating abilities, which is related to decrease in mitotic cells and inhibition of stem cell-related genes. RNAi-HSP60 disrupts the structure of the mitochondria and inhibits the mitochondrial-related genes, which mainly occur in intestinal tissues. RNAi-HSP60 also damages the integrity of intestinal tissues and downregulates intestine-expressed genes. More interestingly, RNAi-HSP60 upregulates the expression of the cathepsin L-like gene, which may be the reason for head regression and necrotic-like cell death. Taking these points together, we propose a model illustrating the relationship between neoblasts and intestinal cells, and also highlight the essential role of the intestinal system in planarian regeneration and tissue homeostasis.

A dynamic DNA nanosponge for triggered amplification of gene-photodynamic modulation.

Nucleic acid therapeutics has reached clinical utility through modulating gene expression. As a potential oligonucleotide drug, DNAzyme has RNA-cleaving activity for gene silencing, but faces challenges due to the lack of a safe and effective delivery vehicle and low in vivo catalytic activity. Here we describe DNAzyme-mediated gene regulation using dynamic DNA nanomaterials with intrinsic biocompatibility, stability, tumor-targeted delivery and uptake, and self-enhanced efficacy. We assemble programmable DNA nanosponges to package and deliver diverse nucleic acid drugs and therapeutic agents such as aptamer, DNAzyme and its cofactor precursor, and photosensitizer in one pot through the rolling circle amplification reaction, formulating a controllable nanomedicine using encoded instructions. Upon environmental stimuli, DNAzyme activity increases and RNA cleavage accelerates by a supplementary catalytic cofactor. In addition, this approach induces elevated O2 and 1O2 generation as auxiliary treatment, achieving simultaneously self-enhanced gene-photodynamic cancer therapy. These findings may advance the clinical trial of oligonucleotide drugs as tools for gene modulation.

Whole-genome sequencing and antimicrobial resistance analysis of multidrug-resistant Aeromonas veronii strain JC529 from a common carp.

OBJECTIVES: Aeromonas veronii can cause infections in humans and a wide variety of aquatic and terrestrial animals as well as causing serious economic losses in aquaculture worldwide. Aeromonas veronii strain JC529 was isolated from an infected common carp in a fish pond in Jilin Province. In this study, we identified the multidrug resistance genes and traced the source of the strain in order to lay the foundation for research on the resistance mechanisms of other Aeromonas isolates. METHODS: The isolated strain was sequenced using PacBio RS II and Illumina HiSeq 4000 platforms. Corrected reads were assembled using Celera and Falcon software and genes were predicted using Glimmer software. Seven databases were used for general function annotation. Virulence factors and resistance genes were identified based on the core data set in the VFDB and ARDB databases. Concurrently, 68 publicly available A. veronii genomes (including A. veronii JC529) were compared to reveal the clustering relationship of JC529. RESULTS: Aeromonas veronii strain JC529 has a circular chromosome of 4 834 659 bp with a GC content of 59.64%, including 4264 protein-coding genes, 2 prophages, 482 virulence factors and 27 antibiotic resistance genes, indicating that strain JC529 is a multidrug-resistant strain. The phylogenetic tree showed that strains JC529 and NS, PDB, AG5.28.6 and VCK1 appear to be inherited from a common ancestor and affect aquaculture in China and Greece. CONCLUSION: Strain JC529 is a multidrug-resistant A. veronii strain and has been inherited from a common ancestor with Greece.

[Functional analysis of autophagy-related gene Atg6 in planarian central nervous system regeneration].

Autophagy-related gene 6 (Atg6) plays an essential role in autophagy, and loss of its function impairs neurogenesis. Planarian is a good model for the study of the central nervous system (CNS) regeneration. It can regenerate a new head de novo in 1 week following decapitation. Therefore, functional analysis of Atg6 in planarian CNS regeneration is very important for understanding of autophagy in the regulation of neurogenesis. In this work, we reported the molecular characteristics of Atg6 in Dugesia japonica (DjAtg6) for the first time and examined its function by RNAi. The full-length cDNA of DjAtg6 is 1366 bp encoding 423 amino acids. The deduced amino sequence of DjAtg6 contains the coil-coil domain and ß-α-repeated autophagy-specific domain shared by ATG6/Beclin 1 family. Following amputation before and after the pharynx, DjAtg6 transcripts increased and were mainly distributed in the newly regenerated brain structure. RNAi-DjAtg6 delayed planarian head regeneration with a small size of brain, and decreased the expression levels of neural-related genes. In addition, our results revealed that RNAi-DjAtg6 did not affect the stem cell proliferation, but down-regulated the cell migration-related genes mmp1 and mmp2. Furthermore, RNAi-mmp1 and RNAi-mmp2 delayed planarian head regeneration. Therefore, our results suggest that DjAtg6 is important for planarian CNS regeneration. The abnormal CNS regeneration caused by RNAi-DjAtg6 may be related to cell migration, but the detailed mechanism needs to be further investigated.

Identification of a potential tissue-specific biomarker cathepsin L-like gene from the planarian Dugesia japonica: Molecular cloning, characterization, and expression in response to heavy metal exposure.

Heavy metal pollution is a global health issue affecting people worldwide, and the exploration of sensitive biomarkers to assess the toxicity of heavy metals is an important work for researchers. Cathepsin L, role as a tissue-specific biomarker to assess the biological effects of environmental pollutants, has not received much attention. In this work, the full-length cDNA of cathepsin L gene from the planarian Dugesia japonica (designated DjCatL) was cloned by rapid amplification of cDNA ends (RACE) technique. The cDNA sequence of DjCatL is 1161 bp, which encodes a protein of 346 amino acids with a molecular weight of 39.03 kDa. Sequence analysis revealed that DjCatL contains highly conserved ERF/WNIN, GNFD, and GCXGG motifs, which are the features of the cathepsin L protein family. Whole-mount in situ hybridization (WISH) results revealed that the transcripts of DjCatL are specifically distributed in the intestinal system, suggesting that this gene is related to food digestion in planarians. Both quantitative polymerase chain reaction (qPCR) and WISH results revealed that the transcriptional levels of DjCatL are inhibited significantly by heavy metal (Cd2+, Hg2+, and Cu2+) exposure in a dose-dependent manner. Therefore, we proposed that cathepsin L can be used as a tissue-specific biomarker to assess the heavy metal pollution in the aquatic environment.

Identification of Autophagy-Related Gene 7 and Autophagic Cell Death in the Planarian Dugesia japonica.

Planarians undergo continuous body size remodeling under starvation or during regeneration. This process likely involves autophagy and autophagic cell death, but this hypothesis is supported by few studies. To test this hypothesis, we cloned and characterized autophagy-related gene 7 (Atg7) from the planarian Dugesia japonica (DjAtg7). The full-length cDNA of DjAtg7 measures 2272 bp and includes a 2082-bp open reading frame encoding 693 amino acids with a molecular weight of 79.06 kDa. The deduced amino acid sequence of DjAtg7 contains a conserved ATP-binding site and a catalytic active site of an E1-like enzyme belonging to the ATG7 superfamily. DjAtg7 transcripts are mainly expressed in intestinal tissues of the intact animals. After amputation, DjAtg7 was highly expressed at the newly regenerated intestinal branch on days 3-7 of regeneration and in the old tissue of the distal intestinal branch on day 10 of regeneration. However, knockdown of DjAtg7 by RNAi did not affect planarian regeneration and did not block autophagosome formation, which indicates that autophagy is more complex than previously expected. Interestingly, TEM clearly confirmed that autophagy and autophagic cell death occurred in the old tissues of the newly regenerated planarians and clearly revealed that the dying cell released vesicles containing cellular cytoplasmic contents into the extracellular space. Therefore, the autophagy and autophagic cell death that occurred in the old tissue not only met the demand for body remodeling but also met the demand for energy supply during planarian regeneration. Collectively, our work contributes to the understanding of autophagy and autophagic cell death in planarian regeneration and body remodeling.