Morphological and Genetic Mechanisms of Regeneration in Hemichordates
Ontology highlight
ABSTRACT:
ORGANISM(S): Ptychodera flava
PROVIDER: GSE70295 | GEO | 2015/06/26
SECONDARY ACCESSION(S): PRJNA288180
REPOSITORIES: GEO
Similar Datasets
Project description:Analysis of gene expression level changes during the regeneration of the hemichordate posterior during the first 96 hours of regeneration. Animals were bisected, then collected at eight experimental timepoints - 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96 hours, with a minimum of four replicates for each timepoint. Additionally, four healthy and intact animals were bisected and immediately collected to serve as reference controls.
2015-06-26 | E-GEOD-70295 | biostudies-arrayexpress
Project description:X1 neoblasts (G2/S/M cells) were isolated by FACS from injury site-proximal tissue in a timeseries during head (anterior) and tail (posterior) regeneration in Schmidtea mediterranea 24 samples: 2 treatments (head versus tail regeneration), 3 timepoints (0,24,48,72 hours post amputation), 3 biological replicates each condition
2014-05-01 | E-GEOD-56178 | biostudies-arrayexpress
Project description:X1 neoblasts (G2/S/M cells) were isolated by FACS from injury site-proximal tissue in a timeseries during head (anterior) and tail (posterior) regeneration in Schmidtea mediterranea
2014-05-01 | GSE56178 | GEO
Project description:Regeneration of missing body parts can be observed in diverse animal phyla, but it remains unclear to which extent these capacities rely on shared or divergent principles. Research into this question requires detailed knowledge about the involved molecular and cellular principles in suitable reference models. By combining single-cell RNA sequencing and mosaic transgenesis in the marine annelid Platynereis dumerilii, we map cellular profiles and lineage restrictions during posterior regeneration. Our data reveal cell-type specific injury responses, re-expression of positional identity factors, and the re-emergence of stem cell signatures in multiple cell populations. Epidermis and mesodermal coelomic tissue produce distinct putative posterior stem cells (PSCs) in the emerging blastema. A novel mosaic transgenesis strategy reveals both developmental compartments and lineage restrictions during regenerative growth. Our work supports the notion that posterior regeneration involves dedifferentiation, and reveals molecular and mechanistic parallels between annelid and vertebrate regeneration.
2024-09-21 | GSE277281 | GEO
Project description:To identify changes in metabolites that correlate with progression of tail regeneration, we collected a timecourse of tissues containing 250 um of tissue anterior to the wound site as well as all regenerating tissue at 0, 3, and 24 hours post amputation. We also collected the posterior 500 um of the developing tail to represent the metabolic profile of uninjured tissues. Tissues from 25 individuals were collected and frozen in more than 5-8 minutes per replicate before processing as in the methods. 104 metabolites were identified in these samples and relative peak intensities were compared to identify changes in abundance corresponding to regeneration. 42 differentially abundant metabolites were found using MetaboAnalyst, the majority of which were increased 24 hours post amputation. Further investigation of these 24 hours post amputation enriched metabolites revealed that these metabolites were largely associated with increased growth and nucleotide metabolism. This finding is in line with the growth of new tissue seen at this timepoint and also suggests that generation of nucleotides are a major factor in sustaining this growth.
2022-08-03 | ST002271 | MetabolomicsWorkbench
Project description:Variability of regenerative potential among animals has long perplexed biologists. Based on their amazing regenerative abilities, planarians have become important models for understanding the molecular basis of regeneration; however, planarian species with limited regenerative abilities are also found. Despite the importance of understanding the differences between closely related, regenerating and non-regenerating organisms, few studies have focused on the evolutionary loss of regeneration, and the molecular mechanisms leading to such regenerative loss remain obscure. Here we examine Procotyla fluviatilis, a planarian with restricted ability to replace missing tissues, utilizing next-generation sequencing to define the gene expression programs active in regeneration-permissive and regeneration-deficient tissues. We found that Wnt signaling is aberrantly activated in regeneration-deficient tissues. Remarkably, down-regulation of canonical Wnt signaling in regeneration-deficient regions restores regenerative abilities: blastemas form and new heads regenerate in tissues that normally never regenerate. This work reveals that manipulating a single signaling pathway can reverse the evolutionary loss of regenerative potential. RNA-seq experiments to identify gene expression changes following amputation in body regions with variable regenerative potential. Adult Procotyla fluviatilis were amputated at sites either anterior or posterior to the pharynx. After 24 hours post-amputation, tissues near the amputation site were excised and RNA was extracted. Similar tissues were excised from uncut control animals. Samples were processed for RNA-seq using Illumina procedures. We generated a de novo P. fluviatilis transcriptome and used RNA sequencing (RNA-seq) to characterize transcripts from excised tissue fragments in Reg+ and Reg- body regions 24 hours post-amputation. We performed parallel analyses on tissues excised from intact animals at identical body regions to account for regional differences in transcripts, thereby identifying changes resulting from amputation. Samples A1-A3 = Regeneration-proficient (Reg+) tissue excision 24 hours after amputation. Samples B1-B3 = Tissue excision from regeneration-proficient (Reg+) region but not amputated. Samples C1-C3 = Tissue excision from regeneration-deficient (Reg-) tissues 24 hours after amputation. Samples D1, D3-D4 = Tissue excision from regeneration-deficient (Reg-) region that was not amputated.
2013-07-04 | E-GEOD-48497 | biostudies-arrayexpress
Project description:In contrast to humans, many amphibians are able to rapidly and completely regenerate complex tissues, including complete appendages. Following tail amputation, Xenopus tropicalis tadpoles quickly regenerate muscle, spinal cord, cartilage, vasculature and skin, all properly patterned in three dimensions. To better understand the molecular basis of this regenerative competence, we performed a transcriptional analysis of regeneration using RNA-Seq. We profiled the transcriptome at 6 timepoints during tail regeneration, and used clustering analysis to identify biological processes that are prioritized during different transitions in the regeneration process. Our work expands significantly on previous expression analyses of tail regeneration. We are able to refine the windows during which many key biological signaling processes act, including embryonic patterning signals, immune responses, bioelectrical signaling and apoptosis. By including multiple timepoints within the first 24 hours post-amputation, we have also identified new processes that are highly prioritized early in regeneration, including axonogenesis, chemotaxis, and RNA metabolism. Our work provides a deep database for researchers interested in appendage regeneration, and highlights new avenues for further study.
2017-01-30 | GSE88975 | GEO
Project description:For a damaged tissue to regenerate, the injured site must repair the wound, proliferate, and restore the correct patterning and cell types. We found that Zelda, a pioneer transcription factor largely known for its role in embryonic zygotic genome activation, is dispensable for normal wing development but crucial for wing disc patterning during regeneration. Impairing Zelda function during disc regeneration resulted in adult wings with a plethora of cell fate errors, affecting the veins, margins, and posterior compartment identity. Using CUT&RUN, we identified and validated targets of Zelda including the cell fate genes cut, Delta and achaete, which failed to return to their normal expression patterns upon loss of Zelda. In addition, Zelda controls expression of factors previously established to preserve cell fate during regeneration like taranis and osa, which stabilizes engrailed expression during regeneration, thereby preserving posterior identity. Finally, Zelda ensures proper expression of the integrins encoded by multiple edematous wings and myospheroid during regeneration to prevent blisters in the resulting adult wing. Thus, Zelda is crucial for maintaining cell fate and structural architecture of the regenerating tissue.
2024-06-26 | GSE268674 | GEO
Project description:The objective of this study is to evaluate for the first time not only the impact of neoadjuvant chemotherapy on clinical outcome, but also on liver regeneration after liver resection.
| 2063066 | ecrin-mdr-crc
Project description:This spatio-temporal model explores tissue polarity re-organization during planarian double-head formation upon regeneration with beta-catenin-1 RNAi treatment. Initial conditions for A and M polarity fields are chosen near the wild type pattern and the first 100 time steps are used to establish the typical wild type splay pattern. The induction of the ectopic head occurs at time-step 100 (interpreted as tail amputation time) at the position where the former tail was (right end), subsequently affects the nearby tissue with some lag and then re-polarizes the posterior half of the tissue from time-step 200 onward. Of these polarity fields, A represents the anterior-posterior polarization system provided by the core PCP pathway, M represents the medio-lateral polarization system provided by the Ft/Ds pathway and P represents the resulting superimposed and normalized polarization. P can be compared to the observable polarity data of ciliary rootlets. This simulation reproduces Figure 4D of the referenced paper. Parameter values correspond to the beta-catenin-1(RNAi) pattern as given in Table S2 of the referenced paper. The model file is in MorpheusML format and can be opened in the free, open-source multicellular modeling software Morpheus (https://morpheus.gitlab.io) to simulate the time course (movie) of the spatio-temporal dynamics.
2021-10-06 | MODEL2110050001 | BioModels