Preclinical Molecular Signatures of Spinal Cord Functional Restoration: Optimizing the Metamorphic Axolotl (Ambystoma mexicanum) Model in Regenerative Medicine

Can Microbiome Modulate Regenerative Capacity? A Comparative Microbiome Study Reveals a Dominant Presence of Flavobacteriaceae in Blastema Tissue During Axolotl Limb Regeneration

The axolotl (Ambystoma mexicanum) is renowned for its remarkable regenerative capabilities, which are not diminished by the transition from a neotenic to a metamorphic state. This study explored the microbiome dynamics in axolotl limb regeneration by examining the microbial communities present in neotenic and metamorphic axolotls at two critical stages of limb regeneration: pre-amputation and during blastema formation. Utilizing 16S rRNA amplicon sequencing, we investigated the variations in microbiome profiles associated with different developmental and regenerative states. Our findings reveal a distinct separation in the microbiome profiles of neotenic and metamorphic samples, with a clear demarcation in microbial composition at both the phylum and genus levels. In neotenic 0DPA samples, Proteobacteria and Firmicutes were the most abundant, whereas in neotenic 7DPA samples, Proteobacteria and Bacteroidetes dominated. Conversely, metamorphic samples displayed a higher abundance of Firmicutes and Bacteroidetes at 0DPA and Proteobacteria and Firmicutes at 7DPA. Alpha and beta diversity analyses, along with dendrogram construction, demonstrated significant variations within and between the sample groups, suggesting a strong influence of both developmental stage and regenerative state on the microbiome. Notably, Flavobacterium and Undibacterium emerged as distinctive microbial entities in neotenic 7DPA samples, highlighting potential key players in the microbial ecology of regeneration. These findings suggest that the axolotl's microbiome is dynamically responsive to blastema formation, and they underscore the potential influence of microbial communities on the regeneration process. This study lays the groundwork for future research into the mechanisms by which the microbiome may modulate regenerative capacity.

The Dynamic Landscapes of Circular RNAs in Axolotl, a Regenerative Medicine Model, with Implications for Early Phase of Limb Regeneration

Circular RNAs (circRNAs) are of relevance to regenerative medicine and play crucial roles in post-transcriptional and translational regulation of biological processes. circRNAs are a class of RNA molecules that are formed through a unique splicing process, resulting in a covalently closed-loop structure. Recent advancements in RNA sequencing technologies and specialized computational tools have facilitated the identification and functional characterization of circRNAs. These molecules are known to exhibit stability, developmental regulation, and specific expression patterns in different tissues and cell types across various organisms. However, our understanding of circRNA expression and putative function in model organisms for regeneration is limited. In this context, this study reports, for the first time, on the repertoire of circRNAs in axolotl, a widely used model organism for regeneration. We generated RNA-seq data from intact limb, wound, and blastema tissues of axolotl during limb regeneration. The analysis revealed the presence of 35,956 putative axolotl circRNAs, among which 5331 unique circRNAs exhibited orthology with human circRNAs. In silico data analysis underlined the potential roles of axolotl circRNAs in cell cycle, cell death, and cell senescence-related pathways during limb regeneration, suggesting the participation of circRNAs in regulation of diverse functions pertinent to regenerative medicine. These new observations help advance our understanding of the dynamic landscape of axolotl circRNAs, and by extension, inform future regenerative medicine research and innovation that harness this model organism.

Downregulation of Yap1 during limb regeneration results in defective bone formation in axolotl

The Hippo pathway plays an imperative role in cellular processes such as differentiation, regeneration, cell migration, organ growth, apoptosis, and cell cycle. Transcription coregulator component of Hippo pathway, YAP1, promotes transcription of genes involved in cell proliferation, migration, differentiation, and suppressing apoptosis. However, its role in epimorphic regeneration has not been fully explored. The axolotl is a well-established model organism for developmental biology and regeneration studies. By exploiting its remarkable regenerative capacity, we investigated the role of Yap1 in the early blastema stage of limb regeneration. Depleting Yap1 using gene-specific morpholinos attenuated the competence of axolotl limb regeneration evident in bone formation defects. To explore the affected downstream pathways from Yap1 down-regulation, the gene expression profile was examined by employing LC-MS/MS technology. Based on the generated data, we provided a new layer of evidence on the putative roles of increased protease inhibition and immune system activities and altered ECM composition in diminished bone formation capacity during axolotl limb regeneration upon Yap1 deficiency. We believe that new insights into the roles of the Hippo pathway in complex structure regeneration were granted in this study.

Axolotl: A resourceful vertebrate model for regeneration and beyond

The regenerative capacity varies significantly among the animal kingdom. Successful regeneration program in some animals results in the functional restoration of tissues and lost structures. Among the highly regenerative animals, axolotl provides multiple experimental advantages with its many extraordinary characteristics. It has been positioned as a regeneration model organism due to its exceptional renewal capacity, including the internal organs, central nervous system, and appendages, in a scar-free manner. In addition to this unique regeneration ability, the observed low cancer incidence, its resistance to carcinogens, and the reversing effect of its cell extract on neoplasms strongly suggest its usability in cancer research. Axolotl's longevity and efficient utilization of several anti-aging mechanisms underline its potential to be employed in aging studies.

The amazing and anomalous axolotls as scientific models

Ambystoma mexicanum (axolotl) embryos and juveniles have been used as model organisms for developmental and regenerative research for many years. This neotenic aquatic species maintains the unique capability to regenerate most, if not all, of its tissues well into adulthood. With large externally developing embryos, axolotls were one of the original model species for developmental biology. However, increased access to, and use of, organisms with sequenced and annotated genomes, such as Xenopus laevis and tropicalis and Danio rerio, reduced the prevalence of axolotls as models in embryogenesis studies. Recent sequencing of the large axolotl genome opens up new possibilities for defining the recipes that drive the formation and regeneration of tissues like the limbs and spinal cord. However, to decode the large Ambystoma mexicanum genome will take a herculean effort, community resources, and the development of novel techniques. Here, we provide an updated axolotl-staging chart ranging from 1-cell stage to immature adult paired with a perspective on both historical and current axolotl research that spans from their use in early studies of development to the recent cutting-edge research, employment of transgenesis, high resolution imaging, and study of mechanisms deployed in regeneration. This article is protected by copyright. All rights reserved.

Mexican Axolotl Optimization: A Novel Bioinspired Heuristic

When facing certain problems in science, engineering or technology, it is not enough to find a solution, but it is essential to seek and find the best possible solution through optimization. In many cases the exact optimization procedures are not applicable due to the great computational complexity of the problems. As an alternative to exact optimization, there are approximate optimization algorithms, whose purpose is to reduce computational complexity by pruning some areas of the problem search space. To achieve this, researchers have been inspired by nature, because animals and plants tend to optimize many of their life processes. The purpose of this research is to design a novel bioinspired algorithm for numeric optimization: the Mexican Axolotl Optimization algorithm. The effectiveness of our proposal was compared against nine optimization algorithms (artificial bee colony, cuckoo search, dragonfly algorithm, differential evolution, firefly algorithm, fitness dependent optimizer, whale optimization algorithm, monarch butterfly optimization, and slime mould algorithm) when applied over four sets of benchmark functions (unimodal, multimodal, composite and competition functions). The statistical analysis shows the ability of Mexican Axolotl Optimization algorithm of obtained very good optimization results in all experiments, except for composite functions, where the Mexican Axolotl Optimization algorithm exhibits an average performance.