Crustacean leg regeneration restores cell diversity
Ontology highlight
ABSTRACT:
ORGANISM(S): Parhyale hawaiensis
PROVIDER: GSE206980 | GEO | 2022/06/30
REPOSITORIES: GEO
Similar Datasets
Project description:Crustacean leg regeneration restores cell diversity
| PRJNA853193 | ENA
Project description:Regenerating animals have the ability to reproduce body parts that were originally made in the embryo and subsequently lost due to injury. Understanding whether the process of regeneration mirrors development is an open question in most regenerative species. Here we take a transcriptomics approach to examine to what extent leg regeneration shows the same temporal patterns of gene expression as leg development in the embryo, in the crustacean Parhyale hawaiensis. We find that leg development in the embryo shows stereotypic temporal patterns of gene expression. In contrast, global patterns of gene expression during leg regeneration show a high degree of variation, related to the physiology of individual animals. A major driver of this variation is the molting cycle. After dissecting the transcriptional signals of individual physiology from regeneration, we obtain temporal signals that mark distinct phases of leg regeneration. Comparing the transcriptional dynamics of development and regeneration we find that, although both processes use largely the same genes, the temporal patterns in which these gene sets are deployed are different and cannot be systematically aligned.
2022-06-15 | GSE196485 | GEO
Project description:Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-Seq, an improved form of the Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq), to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis, and limb development. In addition, we use short- and long-read RNA-Seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We leverage a variety of bioinformatic tools to discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions, and correlate gene expression with accessibility.
2022-05-25 | GSE197886 | GEO
Project description:The study has been described in the following paper: Gianni Parise, Stuart M. Phillips, Jan J. Kaczor and Mark A. Tarnopolsky (2005). Antioxidant enzyme activity is up-regulated after unilateral resistance exercise training in older adults. Free Radical Biology and Medicine, Volume 39, Issue 2, 15 July 2005, Pages 289-295 We cite the following three paragraphs from this paper: "MATERIALS AND METHODS Subjects Twelve men (71.2 ± 6.5 y) volunteered to participate in a 12 week uni-lateral leg resistance training program (Table 1). All subjects underwent a thorough screening process before being admitted into the study. Subjects were first screened by telephone, and were then subject to a medical evaluation. Consent from their family physician was required, and then all potential subjects underwent a resting electrocardiogram, and a sub-maximal graded exercise test on a bicycle ergometer witih a 12-lead ECG. Exclusion criteria included: evidence of coronary hear disease; congestive heart failure; uncontrolled hypertension; chronic obstructive pulmonary disease; diabetes mellitus; renal failure; major orthopaedic disability; and smoking. None of the subjects had ever participated in a structured exercise program. After subjects were advised of the benefits and risks of participation, subjects gave their written informed consent. The study was approved by the McMaster University and Hamilton Health Sciences Research Ethics Board and conferred to the principles of the declaration of Helsinki. Exercise Training Resistance training was performed three times weekly on non-consecutive days (Monday, Wednesday, and Friday) for 12 weeks, under strict supervision. Prior to and after each training session subjects were required to perform passive stretching. Resistance exercise for each session consisted of 3 sets of 10 repetitions for each of leg press and leg extension. Training progressed from one set of each exercise at 50% of the initial 1 repetition maximum (1RM) to 3 sets at 80% of 1RM over the training period. Training logs were kept to record the volume and intensity of each session. The 1RM was re-evaluated every 2 weeks, and the training load was adjusted accordingly. All exercises were performed on universal strength training equipment (Universal Gym Equipment, Inc., Cedar Rapids, Iowa). Muscle Biopsy A muscle biopsy was taken from the vastus lateralis muscle of both legs before as well as after the training period, 20 cm proximal to the knee joint using a modified Bergström needle (5 mm diameter) with suction modification. The biopsy specimen was dissected of fat and connective tissue and immediately frozen in liquid nitrogen. All samples were stored at -80 °C for subsequent analysis. All subjects were required to abstain from strenuous physical activity for 48 hours prior to the testing session. The non-trained leg performed an acute bout of exercise at the same relative intensity of the training leg to allow for the determination of the effect of training and the effect of acute resistance exercise." Additional Notes: 1) The samples of 8 out 12 were used in the gene expression study. 2) The 2 factors in this study are: 2.1) Leg - Left or Right 2.2) Training - Baseline: samples taken on each leg before exercise - Resistance Training: one of the legs was subject to resistance training followed by acute exercise - Acute Exercise: the other leg had only the acute exercise 3) The baseline samples will be used for right versus left leg comparison to see variance between legs for human experimentation technical issues. The samples from Resistance or Acute Exercise will be compared to corresponding baseline samples to evaluate the effect of both exercise programs on gene expression.
2007-06-07 | E-MEXP-740 | biostudies-arrayexpress
Project description:Proteogenomics of Parhyale hawaiensis ovaries to define the core-proteome of female reproductive tissues from crustacean amphipods
2015-09-21 | PXD002310 | Pride
Project description:The embryo of the crustacean Parhyale hawaiensis has a total, unequal and invariant early cleavage. It specifies cell fates earlier than other arthropods like Drosophila, as individual blastomeres of the 8-cell stage are allocated to the germ layers and the germline. Furthermore, the 8-cell stage is amenable to embryological manipulations. These unique features make Parhyale a suitable system for elucidating germ layer specification in arthropods. Since asymmetric localization of maternally provided RNA is a widespread mechanism to specify early cell fates, we asked whether this is also true for Parhyale. A candidate gene approach did not find RNAs that are asymmetrically distributed at the 8-cell stage. Therefore, we designed a high-density microarray from 9400 recently sequenced ESTs (1) to identify maternally provided RNAs and (2) to find RNAs that are differentially distributed among cells of the 8-cell stage. Maternal-zygotic transition takes place around the 32-cell stage, i.e. after the specification of germ layers. By comparing a pool of RNAs from early embryos without zygotic transcription to zygotic RNAs of the germband, we found that more than 15% of the targets on the array were enriched in the maternal transcript pool. A screen for asymmetrically distributed RNAs at the 8-cell stage revealed 129 transcripts, which were associated with germ-layer-specific GO-terms. Cross-correlation analysis of the microarray experiments indicated that half of the asymmetrically distributed RNAs at the 8-cell stage are degraded before the start of zygotic transcription. Finally, we performed knock-down experiments for two of these genes and observed cell-fate-related defects of embryonic development.
2012-11-19 | GSE41887 | GEO
Project description:The embryo of the crustacean Parhyale hawaiensis has a total, unequal and invariant early cleavage. It specifies cell fates earlier than other arthropods like Drosophila, as individual blastomeres of the 8-cell stage are allocated to the germ layers and the germline. Furthermore, the 8-cell stage is amenable to embryological manipulations. These unique features make Parhyale a suitable system for elucidating germ layer specification in arthropods. Since asymmetric localization of maternally provided RNA is a widespread mechanism to specify early cell fates, we asked whether this is also true for Parhyale. A candidate gene approach did not find RNAs that are asymmetrically distributed at the 8-cell stage. Therefore, we designed a high-density microarray from 9400 recently sequenced ESTs (1) to identify maternally provided RNAs and (2) to find RNAs that are differentially distributed among cells of the 8-cell stage. Maternal-zygotic transition takes place around the 32-cell stage, i.e. after the specification of germ layers. By comparing a pool of RNAs from early embryos without zygotic transcription to zygotic RNAs of the germband, we found that more than 15% of the targets on the array were enriched in the maternal transcript pool. A screen for asymmetrically distributed RNAs at the 8-cell stage revealed 129 transcripts, which were associated with germ-layer-specific GO-terms. Cross-correlation analysis of the microarray experiments indicated that half of the asymmetrically distributed RNAs at the 8-cell stage are degraded before the start of zygotic transcription. Finally, we performed knock-down experiments for two of these genes and observed cell-fate-related defects of embryonic development.
2012-11-19 | GSE41886 | GEO