Post-amputation reactive oxygen species production is necessary for axolotls limb regeneration

Impacts of severity and region of gill tissue resection on regeneration in Atlantic salmon (Salmo salar)

In a previous study, we demonstrated successful regeneration of Atlantic salmon gill tissue following up to 50 % filament resection. The present study explored 1) the capacity of gill tissue to regenerate following more severe trauma, 2) if regeneration potential varies across regions of the arch, and 3) how tissue loss impacts the physiology of neighboring unresected filaments. Fish were divided between two resected groups and a control non-resected one. In resection group-1, fish underwent 50 % and 75 % resection in the ventral and medial-dorsal regions of the first arch, while in resection group-2, the location of resection levels was reversed. The degree of filament regeneration and physiology of unresected filaments were measured at 4, 12 and 20 weeks-post-resection (WPR). Overall, the degree of regeneration was significantly higher in 50 % resected filaments relative to 75 % resected filaments. The degree of regeneration did not differ significantly between the resected groups for either of resection levels, suggesting negligible impact of filament location on arch on regeneration. The concentration of oxidized glutathione (GSSG), total glutathione (GSH), and citrate synthase activity (CSA) in intact filaments were comparable between resected and control fish at both 4 and 20 WPR. However, GSH concentration varied among resected fish with those exhibited higher GSH in intact filaments showed lower regeneration of 50 % resected filaments at 20 WPR. Our results indicate that gill tissue loss exceeding 50 % may significantly impair regeneration and that this level of tissue loss is not associated with a compensatory response (e.g. GSSG, GSH, CSA) of neighboring gill tissue.

Regeneration of Lumbriculus variegatus requires post-amputation production of reactive oxygen species

Animals vary in their ability to replace body parts lost to injury, a phenomenon known as restorative regeneration. Uncovering conserved signaling steps required for regeneration may aid regenerative medicine. Reactive oxygen species (ROS) are necessary for proper regeneration in species across a wide range of taxa, but it is unknown whether ROS are essential for annelid regeneration. As annelids are a widely used and excellent model for regeneration, we sought to determine whether ROS play a role in the regeneration of the highly regenerative annelid, Lumbriculus variegatus. Using a ROS-sensitive fluorescent probe we observed ROS accumulation at the wound site within 15 min after amputation; this ROS burst lessened by 6 h post-amputation. Chemical inhibition of this ROS burst delayed regeneration, an impairment that was partially rescued with exogenous ROS. Our results suggest that similar to other animals, annelid regeneration depends upon ROS signaling, implying a phylogenetically ancient requirement for ROS in regeneration.

Antibacterial Activity of AXOTL-13, a Novel Peptide Identified from the Transcriptome of the Salamander Ambystoma mexicanum

Background/Objectives: Antimicrobial peptides are essential molecules in the innate immunity of various organisms and possess a broad spectrum of antimicrobial, antitumor, and immunomodulatory activities. Due to their multifunctionality, they are seen as an alternative for controlling bacterial infections. Although conventional antibiotics have improved health worldwide, their indiscriminate use has led to the emergence of resistant microorganisms. To discover new molecules with antimicrobial activity that could overcome the limitations of traditional antibiotics, this study aimed to identify antimicrobial peptides in Ambystoma mexicanum. Methods: In this study, hypothetical proteins encoded in the Ambystoma mexicanum transcriptome were predicted. These proteins were aligned with peptides reported in the Antimicrobial Peptide Database (APD3) using the Fasta36 program. After identifying peptide sequences with potential antibacterial activity, their expression was confirmed through conventional polymerase chain reaction (PCR) and then chemically synthesized. The antibacterial activity of the synthesized peptides was evaluated against Staphylococcus aureus ATCC 25923 and Escherichia coli ATCC 25922. Results: A new antimicrobial peptide named AXOTL-13 was identified. AXOTL-13 is an amphipathic cationic alpha-helical peptide with the ability to inhibit the growth of Escherichia coli without causing hemolysis in red blood cells, with its action likely directed at the membrane, as suggested by morphological changes observed through scanning electron microscopy. Conclusions: This research is pioneering in evaluating the activity of antimicrobial peptides present in Ambystoma mexicanum and in specifically identifying one of these peptides. The findings will serve as a reference for future research in this field.

Characterization of regeneration initiating cells during Xenopus laevis tail regeneration

BACKGROUND

Embryos are regeneration and wound healing masters. They rapidly close wounds and scarlessly remodel and regenerate injured tissue. Regeneration has been extensively studied in many animal models using new tools such as single-cell analysis. However, until now, they have been based primarily on experiments assessing from 1 day post injury.

RESULTS

In this paper, we reveal that critical steps initiating regeneration occur within hours after injury. We discovered the regeneration initiating cells (RICs) using single-cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells, and their expression signature suggests they are important for modifying the surrounding extracellular matrix thus regulating development. The absence or deregulation of RICs leads to excessive extracellular matrix deposition and defective regeneration.

CONCLUSION

RICs represent a newly discovered transient cell state involved in the initiation of the regeneration process.

Molecular Signatures Integral to Natural Reprogramming in the Pigment Epithelium Cells after Retinal Detachment in Pleurodeles waltl

The reprogramming of retinal pigment epithelium (RPE) cells into retinal cells (transdifferentiation) lies in the bases of retinal regeneration in several Urodela. The identification of the key genes involved in this process helps with looking for approaches to the prevention and treatment of RPE-related degenerative diseases of the human retina. The purpose of our study was to examine the transcriptome changes at initial stages of RPE cell reprogramming in adult newt Pleurodeles waltl. RPE was isolated from the eye samples of day 0, 4, and 7 after experimental surgical detachment of the neural retina and was used for a de novo transcriptome assembly through the RNA-Seq method. A total of 1019 transcripts corresponding to the differently expressed genes have been revealed in silico: the 83 increased the expression at an early stage, and 168 increased the expression at a late stage of RPE reprogramming. We have identified up-regulation of classical early response genes, chaperones and co-chaperones, genes involved in the regulation of protein biosynthesis, suppressors of oncogenes, and EMT-related genes. We revealed the growth in the proportion of down-regulated ribosomal and translation-associated genes. Our findings contribute to revealing the molecular mechanism of RPE reprogramming in Urodela.

Cellular and Molecular Triggers of Retinal Regeneration in Amphibians

Understanding the mechanisms triggering the initiation of retinal regeneration in amphibians may advance the quest for prevention and treatment options for degenerating human retina diseases. Natural retinal regeneration in amphibians requires two cell sources, namely retinal pigment epithelium (RPE) and ciliary marginal zone. The disruption of RPE interaction with photoreceptors through surgery or injury triggers local and systemic responses for retinal protection. In mammals, disease-induced damage to the retina results in the shutdown of the function, cellular or oxidative stress, pronounced immune response, cell death and retinal degeneration. In contrast to retinal pathology in mammals, regenerative responses in amphibians have taxon-specific features ensuring efficient regeneration. These include rapid hemostasis, the recruitment of cells and factors of endogenous defense systems, activities of the immature immune system, high cell viability, and the efficiency of the extracellular matrix, cytoskeleton, and cell surface remodeling. These reactions are controlled by specific signaling pathways, transcription factors, and the epigenome, which are insufficiently studied. This review provides a summary of the mechanisms initiating retinal regeneration in amphibians and reveals its features collectively directed at recruiting universal responses to trauma to activate the cell sources of retinal regeneration. This study of the integrated molecular network of these processes is a prospect for future research in demand biomedicine.

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

BACKGROUND

It is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid contents of proteins. Recently, evidence has accumulated that significant evolutionary transformations could also be associated with the loss/emergence of whole genes. The targeted identification of such genes is a challenging problem for both bioinformatics and evo-devo research.

RESULTS

To solve this problem we propose the WINEGRET method, named after the first letters of the title. Its main idea is to search for genes that satisfy two requirements: first, the desired genes were lost/emerged at the same evolutionary stage at which the phenotypic trait of interest was lost/emerged, and second, the expression of these genes changes significantly during the development of the trait of interest in the model organism. To verify the first requirement, we do not use existing databases of orthologs, but rely purely on gene homology and local synteny by using some novel quickly computable conditions. Genes satisfying the second requirement are found by deep RNA sequencing. As a proof of principle, we used our method to find genes absent in extant amniotes (reptiles, birds, mammals) but present in anamniotes (fish and amphibians), in which these genes are involved in the regeneration of large body appendages. As a result, 57 genes were identified. For three of them, c-c motif chemokine 4, eotaxin-like, and a previously unknown gene called here sod4, essential roles for tail regeneration were demonstrated. Noteworthy, we established that the latter gene belongs to a novel family of Cu/Zn-superoxide dismutases lost by amniotes, SOD4.

CONCLUSIONS

We present a method for targeted identification of genes whose loss/emergence in evolution could be associated with the loss/emergence of a phenotypic trait of interest. In a proof-of-principle study, we identified genes absent in amniotes that participate in body appendage regeneration in anamniotes. Our method provides a wide range of opportunities for studying the relationship between the loss/emergence of phenotypic traits and the loss/emergence of specific genes in evolution.