Mining of potentially stem cell-related miRNAs in planarians.

Stem cells and regenerative medicine have recently become important research topics. However, the complex stem cell regulatory networks involved in various microRNA (miRNA)-mediated mechanisms have not yet been fully elucidated. Planarians are ideal animal models for studying stem cells owing to their rich stem cell populations (neoblasts) and extremely strong regeneration capacity. The roles of planarian miRNAs in stem cells and regeneration have long attracted attention. However, previous studies have generally provided simple datasets lacking integrative analysis. Here, we have summarized the miRNA family reported in planarians and highlighted conservation in both sequence and function. Furthermore, we summarized miRNA data related to planarian stem cells and regeneration and screened potential involved candidates. Nevertheless, the roles of these miRNAs in planarian regeneration and stem cells remain unclear. The identification of potential stem cell-related miRNAs offers more precise suggestions and references for future investigations of miRNAs in planarians. Furthermore, it provides potential research avenues for understanding the mechanisms of stem cell regulatory networks. Finally, we compiled a summary of the experimental methods employed for studying planarian miRNAs, with the aim of highlighting special considerations in certain procedures and providing more convenient technical support for future research endeavors.

Engineered phages in anti-infection and anti-tumor field: A review.

The abuse of antibiotics has led to the widespread emergence of multi-drug resistant bacteria. Phage therapy holds promise for enhancing antibacterial and anti-infection strategies. Traditional bacteriophage therapy employs phage preparations as an alternative to antibiotics for the eradication of bacteria, aiming to achieve the desired clinical outcomes. Modification of phage by transgene or chemical modification overcomes the limitations of traditional bacteriophage therapy, including host spectrum modification, bacterial resistance reversal, antigen presentation, and drug targeted delivery, and thus broadens the application field of phage. This article summarizes the progress of engineered phages in the fields of antibacterial, anti-infective, and anti-tumor therapy. It emphasizes the advantages of engineered phages in antibacterial and anti-tumor treatment, and discusses the widespread potential of phage-based modular design as multifunctional biopharmaceuticals, drug carriers, and other applications.

Evolution and Function of the Notch Signaling Pathway: An Invertebrate Perspective.

The highly conserved Notch signaling pathway affects embryonic development, neurogenesis, homeostasis, tissue repair, immunity, and numerous other essential processes. Although previous studies have demonstrated the location and function of the core components of Notch signaling in various animal phyla, a more comprehensive summary of the Notch core components in lower organisms is still required. In this review, we objectively summarize the molecular features of the Notch signaling pathway constituents, their current expression profiles, and their functions in invertebrates, with emphasis on their effects on neurogenesis and regeneration. We also analyze the evolution and other facets of Notch signaling and hope that the contents of this review will be useful to interested researchers.

Identification and characterization of TatD DNase in planarian Dugesia japonica and its antibiofilm effect.

TatD DNase, a key enzyme in vertebrates and invertebrates, plays a pivotal role in various physiological processes. Dugesia japonica (D. japonica), a flatworm species, has remarkable regenerative capabilities and possesses a simplified immune system. However, the existence and biological functions of TatD DNase in D. japonica require further investigation. Here, we obtained the open reading frame (ORF) of DjTatD and demonstrated its conservation. The three-dimensional structure of DjTatD revealed its active site and binding mechanism. To investigate its enzymological properties, we overexpressed, purified, and characterized recombinant DjTatD (rDjTatD). We observed that DjTatD was primarily expressed in the pharynx and its expression could be significantly challenged upon stimulation with lipopolysaccharide, peptidoglycan, gram-positive and gram-negative bacteria. RNA interference results indicated that both DjTatD and DjDN2s play a role in pharyngeal regeneration and may serve as functional complements to each other. Additionally, we found that rDjTatD and recombinant T7DjTatD effectively reduce biofilm formation regardless of their bacterial origin. Together, our results demonstrated that DjTatD may be involved in the planarian immune response and pharyngeal regeneration. Furthermore, after further optimization in the future, rDjTatD and T7DjTatD can be considered highly effective antibiofilm agents.

CD133+ endothelial-like stem cells restore neovascularization and promote longevity in progeroid and naturally aged mice.

The stem cell theory of aging dictates that a decline in the number and/or function of stem cells causes tissue degeneration and aging; however, it still lacks unequivocal experimental support. Here, using lineage tracing and single-cell transcriptomics, we identify a population of CD133+ bone marrow-derived endothelial-like cells (ELCs) as potential endothelial progenitor cells, which contribute to tubular structures in vitro and neovascularization in vivo. We demonstrate that supplementation with wild-type and young ELCs respectively restores neovascularization and extends lifespan in progeric and naturally aged mice. Mechanistically, we identify an upregulation of farnesyl diphosphate synthase (FDPS) in aged CD133+ ELCs-a key enzyme in isoprenoid biosynthesis. Overexpression of FDPS compromises the neovascularization capacity of CD133+ ELCs, whereas FDPS inhibition by pamidronate enhances neovascularization, improves health measures and extends lifespan in aged mice. These findings highlight stem cell-based strategies for the treatment of progeria and age-related pathologies.

The Physiological Function of nNOS-Associated CAPON Proteins and the Roles of CAPON in Diseases.

In this review, the structure, isoform, and physiological role of the carboxy-terminal PDZ ligand of neuronal nitric oxide synthase (CAPON) are summarized. There are three isoforms of CAPON in humans, including long CAPON protein (CAPON-L), short CAPON protein (CAPON-S), and CAPON-S' protein. CAPON-L includes three functional regions: a C-terminal PDZ-binding motif, carboxypeptidase (CPE)-binding region, and N-terminal phosphotyrosine (PTB) structural domain. Both CAPON-S and CAPON-S' only contain the C-terminal PDZ-binding motif. The C-terminal PDZ-binding motif of CAPON can bind with neuronal nitric oxide synthase (nNOS) and participates in regulating NO production and neuronal development. An overview is given on the relationship between CAPON and heart diseases, diabetes, psychiatric disorders, and tumors. This review will clarify future research directions on the signal pathways related to CAPON, which will be helpful for studying the regulatory mechanism of CAPON. CAPON may be used as a drug target, which will provide new ideas and solutions for treating human diseases.

DjFARP Contributes to the Regeneration and Maintenance of the Brain through Activation of DjRac1 in Dugesia japonica.

FERM, RhoGEF, and Pleckstrin domain protein (FARP) mediated RhoGTPase pathways are involved in diverse biological processes, such as neuronal development and tumorigenesis. However, little is known about their role in neural regeneration. We uncovered for the first time that FARP-Rac1 signaling plays an important role in neural regeneration in Dugesia japonica, a planarian that possesses unparalleled regenerative capacities. The planarian FARP homolog DjFARP was primarily expressed in both intact and regenerating brain and pharynx tissue. Functional studies suggested that downregulation of DjFARP with dsRNA in Dugesia japonica led to smaller brain sizes, defects in brain lateral branches, and loss of cholinergic, GABAergic, and dopaminergic neurons in both intact and regenerating animals. Moreover, the Rho GTPase DjRac1 was shown to play a similar role in neural regeneration and maintenance. Rac1 activation assay showed that DjFARP acts as a guanine nucleotide exchange factor (GEF) for DjRac1. Together, these findings indicate that the brain defects seen in DjFARP knockdown animals may be attributable to DjRac1 inactivation. In conclusion, our study demonstrated that DjFARP-DjRac1 signaling was required for the maintenance and proper regeneration of the brain in Dugesia japonica.

Neodymium affects the generation of reactive oxygen species via GSK-3ß/Nrf2 signaling in the gill of zebrafish.

Rare earth element neodymium (Nd) is widely used in industry and agriculture, which may result in the pollution of aquatic environment. In this study, we exposed zebrafish with 10, 50, and 100 µg/L Nd for four weeks. The results showed that Nd could be accumulated in fish gill and Nd accumulation affected the equilibrium of nutrient elements. Nd decreased the antioxidant enzymes' activity and gene expression level, but enhanced the generation of reactive oxygen species (ROS). Moreover, various concentration of Nd treatments inhibited Nrf2 signaling in gill. To examine the critical role of GSK-3ß/Nrf2 signaling on ROS generation under Nd stress, we further interfered gsk-3ß gene in zebrafish under 100 µg/L Nd exposure. The result showed that gsk-3ß gene interference induced Nrf2 signaling as well as the expression and activity of antioxidant enzymes in fish gill. In all, Nd could be accumulated in fish gill, and the signaling of GSK-3ß/Nrf2 was involved in regulating ROS generation under Nd treatments.

Leveraging aptamers for targeted protein degradation.

Targeted protein degradation (TPD) technologies, particularly proteolysis-targeting chimeras (PROTACs), have emerged as a significant advancement in drug discovery. However, several hurdles - such as the difficulty of identifying suitable ligands for traditionally undruggable proteins, poor solubility and impermeability, nonspecific biodistribution, and on-target off-tissue toxicity - present challenges to their clinical applications. Aptamers are promising ligands for broad-ranging molecular recognition. Utilizing aptamers in TPD has shown potential advantages in overcoming these challenges. Here, we provide an overview of recent developments in aptamer-based TPD, emphasizing their potential to achieve targeted delivery and their promise for the spatiotemporal degradation of undruggable proteins. We also discuss the challenges and future directions of aptamer-based TPD with the goal of facilitating their clinical applications.

WTAP regulates stem cells via TRAF6 to maintain planarian homeostasis and regeneration.

WTAP, a highly conserved Wilms' tumor 1 interacting protein, is involved in a variety of biological processes. However, functional studies of WTAP in planarians have not been reported. In this study, we examined the spatiotemporal expression pattern of planarian DjWTAP and investigated its functions in planarians regeneration and homeostasis. Knocking-down DjWTAP resulted in severe morphological defects leading to lethality within 20 days. Silencing DjWTAP promoted the proliferation of PiwiA+ cells but impaired the lineage differentiation of epidermal, neural, digestive, and excretory cell types, suggesting a critical role for DjWTAP in stem cell self-renewal and differentiation in planarian. To further investigate the mechanisms underlying the defective differentiation, RNA-seq was employed to determine the transcriptomic alterations upon DjWTAP RNA interference. Histone 4 (H4), Histone-lysine N-methyltransferase-SETMAR like, and TNF receptor-associated factor 6 (TRAF6), were significantly upregulated in response to DjWTAP RNAi. Knocking-down TRAF6 largely rescued the defective tissue homeostasis and regeneration resulted from DjWTAP knockdown in planarians, suggesting that DjWTAP maintains planarian regeneration and homeostasis via TRAF6.

Extracellular matrix-regulator MMPA is required for the orderly proliferation of neoblasts and differentiation of ectodermal progenitor cells in the planarian Dugesia japonica.

Matrix metalloproteinases (MMPs) are members of a family of zinc-dependent metallopeptidase proteins that are widely found in plants, animals, and microorganisms. As the regulators of the extracellular matrix and basement membrane, MMPs play an important role in embryogenesis, development, innate immunity, and regeneration. However, the function of MMP family in planarian, a model for regeneration research, is still ambiguous. Here, we cloned 5 MMPs genes from Dugesia japonica and found that DjMMPA was associated with the process of regeneration, neoblasts cell maintenance confusion and destruction. Loss of DjMMPA led to homeostasis confusion and eventually death, owing to neoblasts proliferation disorder. Additionally, DjMMPA RNAi-treated animals had impaired regeneration after amputation. Furthermore, knockdown of DjMMPA had noticeable defects in cell differentiation of ectoderm, especially in eyes and neural progenitor cells, possibly by inhibiting Wnt signaling. Our results suggest that extracellular matrix-regulator MMPA is required for the orderly proliferation of neoblasts and differentiation of ectodermal progenitor cells in the planarian, which provide valuable information for further explorations into the molecular mechanism of MMPS, stem cells, and regeneration.

Characterization of the lipidomic profile of clam Meretrix petechialis in response to Vibrio parahaemolyticus infection.

Vibrio parahaemolyticus is a devastating pathogen of clam Meretrix petechialis, which brings about huge economic losses in aquaculture breeding industry. In our previous study, we have found that Vibrio infection is closely associated with lipid metabolism of clams. In this study, an untargeted lipidomics approach was used to explore the lipid profiling changes upon Vibrio infection. The results demonstrated that the hepatopancreas of clams was composed of five lipid categories including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids and sterol lipids. And the content of lipid classes altered during Vibrio infection, implying that Vibrio infection altered intracellular lipid homeostasis in clams. Meanwhile, a total of 200 lipid species including 82 up-regulated and 118 down-regulated significantly were identified in response to Vibrio infection, of which ceramide (Cer), phosphatidylcholine (PC) and triglyceride (TG) accounted for the largest proportion. Notably, all Cers showed a significantly decreased trend while nearly all TG species were increased significantly during Vibrio infection, which suggested that Cer and TG could be determined as effective biomarkers. Furthermore, these differentially expressed lipid species were enriched in 20 metabolic pathways and sphingolipid metabolism was one of the most enriched pathways. These results evidenced how the lipid metabolism altered in the process of Vibrio infection and opened a new perspective on the response of marine bivalves to pathogen infection.

From marine to freshwater environment: A review of the ecotoxicological effects of microplastics.

Microplastics (MPs) have been widely detected in the world's water, which may pose a significant threat to the ecosystem as a whole and have been a subject of much attention because their presence impacts seas, lakes, rivers, and even the Polar Regions. There have been numerous studies that report direct adverse effects on marine organisms, but only a few have explored their ecological effects on freshwater organisms. In this field, there is still a lack of a systematic overview of the toxic effects and mechanisms of MPs on aquatic organisms, as well as a consistent understanding of the potential ecological consequences. This review describes the fate and impact on marine and freshwater aquatic organisms. Further, we examine the toxicology of MPs in order to uncover the relationship between aquatic organism responses to MPs and ecological disorders. In addition, an overview of the factors that may affect the toxicity effects of MPs on aquatic organisms was presented along with a brief examination of their identification and characterization. MPs were discussed in terms of their physicochemical properties in relation to their toxicological concerns regarding their bioavailability and environmental impact. This paper focuses on the progress of the toxicological studies of MPs on aquatic organisms (bacteria, algae, Daphnia, and fish, etc.) of different trophic levels, and explores its toxic mechanism, such as behavioral alternations, metabolism disorders, immune response, and poses a threat to the composition and stability of the ecosystem. We also review the main factors affecting the toxicity of MPs to aquatic organisms, including direct factors (polymer types, sizes, shapes, surface chemistry, etc.) and indirect factors (persistent organic pollutants, heavy metal ions, additives, and monomer, etc.), and the future research trends of MPs ecotoxicology are also pointed out. The findings of this study will be helpful in guiding future marine and freshwater rubbish studies and management strategies.

Graphene oxide disruption of homeostasis and regeneration processes in freshwater planarian Dugesia japonica via intracellular redox deviation and apoptosis.

The aquatic system is a major sink for engineered nanomaterials released into the environment. Here, we assessed the toxicity of graphene oxide (GO) using the freshwater planarian Dugesia japonica, an invertebrate model that has been widely used for studying the effects of toxins on tissue regeneration and neuronal development. GO not only impaired the growth of normal (homeostatic) worms, but also inhibited the regeneration processes of regenerating (amputated) worms, with LC10 values of 9.86 mg/L and 9.32 mg/L for the 48-h acute toxicity test, respectively. High concentration (200 mg/L) of GO killed all the worms after 3 (regenerating) or 4 (homeostasis) days of exposure. Whole-mount in situ hybridization (WISH) and immunofluorescence analyses suggest GO impaired stem cell proliferation and differentiation, and subsequently caused cell apoptosis and oxidative DNA damage during planarian regeneration. Mechanistic analysis suggests that GO disturbed the antioxidative system (enzymatic and non-enzymatic) and energy metabolism in the planarian at both molecular and genetic levels, thus causing reactive oxygen species (ROS) over accumulation and oxidative damage, including oxidative DNA damage, loss of mitochondrial membrane integrity, lack of energy supply for cell differentiation and proliferation leading to retardance of neuron regeneration. The intrinsic oxidative potential of GO contributes to the GO-induced toxicity in planarians. These data suggest that GO in aquatic systems can cause oxidative stress and neurotoxicity in planarians. Overall, regenerated tissues are more sensitive to GO toxicity than homeostatic ones, suggesting that careful handling and appropriate decisions are needed in the application of GO to achieve healing and tissue regeneration.

Toxicity of ceria nanoparticles to the regeneration of freshwater planarian Dugesia japonica: The role of biotransformation.

Cerium oxide nanoparticles (n-CeO2) have wide applications ranging from industrial to consumer products, which would inevitably lead to their release into the environment. Despite the toxicity of n-CeO2 on aquatic organisms has been largely reported, research on developing organisms is still lacking. In this study, we investigate the toxic effects of n-CeO2 on the stem cells, tissue- and neuro-regeneration, using freshwater planarian Dugesia japonica as a model. Effects of bulk sized (µ-) CeO2 and ionic Ce (Ce3+) were compared with that of n-CeO2 to explore the origin of the toxic effects of n-CeO2. No overt toxicity was observed in µ-CeO2 treatment. n-CeO2 not only impaired the homeostasis of normal planarians, but also inhibited the regeneration processes of regenerated planarians, demonstrated by the inhibited blastema growth, disturbed antioxidant defense system at molecular levels, elevated DNA-damage and decreased stem cell proliferation. Regenerating organisms are more susceptible to n-CeO2 than the normal ones. Ce3+ exhibited significantly higher toxicity than n-CeO2, even though the total Ce uptake is 0.2 % less in Ce3+ than in n-CeO2 treated in planarian. X-ray absorption near edge spectroscopy (XANES) analysis revealed that 12.8 % of n-CeO2 (5.95 mg/kg Ce per planarian) was transformed to Ce3+ after interaction with planarian, suggesting that biotransformation at the nano-bio interface might play an important role in the observed toxicity. Since the biotransformation of n-CeO2 is a slow process, it may cause long-term chronic toxicity to planarians due to the slow while sustained release of toxic Ce3+ ions.

The feedback loop between calcineurin, calmodulin-dependent protein kinase II, and nuclear factor of activated T-cells regulates the number of GABAergic neurons during planarian head regeneration.

Disturbances in the excitatory/inhibitory balance of brain neural circuits are the main source of encephalopathy during neurodevelopment. Changes in the function of neural circuits can lead to depolarization or repeat rhythmic firing of neurons in a manner similar to epilepsy. GABAergic neurons are inhibitory neurons found in all the main domains of the CNS. Previous studies suggested that DjCamkII and DjCaln play a crucial role in the regulation of GABAergic neurons during planarian regeneration. However, the mechanisms behind the regeneration of GABAergic neurons have not been fully explained. Herein, we demonstrated that DjCamkII and DjCaln were mutual negative regulation during planarian head regeneration. DjNFAT exerted feedback positive regulation on both DjCaln and DjCamkII. Whole-mount in situ hybridization (WISH) and fluorescence in situ hybridization (FISH) revealed that DjNFAT was predominantly expressed in the pharynx and parenchymal cells in intact planarian. Interestingly, during planarian head regeneration, DjNFAT was predominantly located in the newborn brain. Down-regulation of DjNFAT led to regeneration defects in the brain including regenerative brain became small and the lateral nerves cannot be regenerated completely, and a decreasein the number of GABAergic neurons during planarian head regeneration. These findings suggest that the feedback loop between DjCaln, DjCamkII, and DjNFAT is crucial for the formation of GABAergic neurons during planarian head regeneration.

Recent trends in T7 phage application in diagnosis and treatment of various diseases.

The T7 phage is a virulent phage hosted by Escherichia coli, which poses no threat to animals and plants. Due to the advantages of small genome, well elucidated functional genomics, fast life cycle, and high stability, T7 phage has been widely used in many fields, including biology and medicine. In this review, we focus on the research of T7 phages in biological sciences and medicine, including the application of T7 phages and T7 phage products, T7 phage display systems, and recombinant T7 phages in the treatment and diagnosis of infectious diseases (bacteria, viruses, parasites) and tumor diseases. In addition, we also introduce the therapeutic application of T7 phage in various diseases such as allergic reaction, Alzheimer's disease, inflammatory reaction, and other diseases, and finally discuss the future direction of T7 phage application in the biomedical field.

Sodium Benzoate Delays the Development of Drosophila melanogaster Larvae and Alters Commensal Microbiota in Adult Flies.

Sodium benzoate (SB), the sodium salt of benzoic acid, is widely used as a preservative in foods and drinks. The toxicity of SB to the human body attracted people's attention due to the excessive use of preservatives and the increased consumption of processed and fast foods in modern society. The SB can inhibit the growth of bacteria, fungi, and yeast. However, less is known of the effect of SB on host commensal microbial community compositions and their functions. In this study, we investigated the effect of SB on the growth and development of Drosophila melanogaster larvae and whether SB affects the commensal microbial compositions and functions. We also attempted to clarify the interaction between SB, commensal microbiota and host development by detecting the response of commensal microbiota after the intervention. The results show that SB significantly retarded the development of D. melanogaster larvae, shortened the life span, and changed the commensal microbial community. In addition, SB changed the transcription level of endocrine coding genes such as ERR and DmJHAMT. These results indicate that the slow down in D. melanogaster larvae developmental timing and shortened life span of adult flies caused by SB intake may result from the changes in endocrine hormone levels and commensal microbiota. This study provided experimental data that indicate SB could affect host growth and development of D. melanogaster through altering endocrine hormone levels and commensal microbial composition.

Roles of ubiquitination in the crosstalk between tumors and the tumor microenvironment (Review).

The interaction between a tumor and the tumor microenvironment (TME) plays a key role in tumorigenesis and tumor progression. Ubiquitination, a crucial post­translational modification for regulating protein degradation and turnover, plays a role in regulating the crosstalk between a tumor and the TME. Thus, identifying the roles of ubiquitination in the process may assist researchers to investigate the mechanisms underlying tumorigenesis and tumor progression. In the present review article, new insights into the substrates for ubiquitination that are involved in the regulation of hypoxic environments, angiogenesis, chronic inflammation­mediated tumor formation, and the function of cancer­associated fibroblasts and infiltrating immune cells (tumor­associated macrophages, T­cells, myeloid­derived suppressor cells, dendritic cells, and natural killer cells) are summarized. In addition, the potential targets of the ubiquitination proteasome system within the TME for cancer therapy and their therapeutic effects are reviewed and discussed.