The Crustacean Model &lt;i&gt;Parhyale hawaiensis&lt;/i&gt;

Paris, Mathilde; Wolff, Carsten; Patel, Nipam H.; Averof, Michalis

doi:10.20944/preprints202106.0018.v1

Cited by 3 publications

(2 citation statements)

References 107 publications

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“…As in other species, the M. rosenbergii putative Ras amino acid sequence is also highly conserved and shares common ancestry with other decapod crustacean species as well as amphibians and rodents. The experimental system used in the present study comprised an embryonic primary cell culture of developed embryos (at the10-12 days stage), which thus contained differentiated cells with native proliferative potential from all germ cell layers, including both dividing and non-dividing cells (Paris et al, 2021). On these cells, we tested the platform recently established in our laboratory by Rotem-Dai (Rotem-Dai et al, 2021), which was used for delivering foreign DNA to hematopoietic primary crustacean cell cultures.…”

Section: Discussionmentioning

confidence: 99%

Enhanced proliferation in a prawn embryonic primary cell culture ectopically expressing mutated Ras

Sudarshan

Weil²,

Rotem-Dai³

et al. 2023

Front. Mar. Sci.

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Crustacean cell line immortalization has gained a great deal of attention in recent decades for both scientific and applied reasons. Our goal in this study was to advance the state of art towards establishing an immortalized cell line by improving the proliferation rates of primary cells isolated from embryos of the giant freshwater prawn Macrobrachium rosenbergii by using a lentivirus expressing the Ras oncogene. The choice of Ras derived from its involvement in various cellular pathways, such as cell growth, differentiation, and survival, and its use as a tool for in-vitro immortalization, e.g., a specific mutated Ras (RasV12) was used to generate an arthropod cell line. Complementarily, in-silico screening of M. rosenbergii transcriptomic libraries for Ras expression indicated that Ras is already expressed at very early stages of embryo development. In the current study, we transduced primary M. rosenbergii embryonic cells with a lentivirus expressing RasV12 by using the white spot syndrome virus (WSSV IE1) promoter. Expression and sequencing (as followed by sequencing cDNA, confocal microscopy and FACS analysis) of the mutated Ras in the transduced cells confirmed that the lentivirus was successfully integrated into the genome. The lenti-MrRas transduction rate was 23% in the total primary cell population and more than 80% in a sub-population of cells with high granularity. Proliferation of lenti-MrRas transfected cells was enhanced to almost 1200% of the seeding density by the end of our experiment (18 days), which was double that of the control. We were thus successful in enhancing the longevity of embryonic primary cell cultures by ectopic expression of the mutated Ras protein, but the improvement was not sufficient for immortalization.

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Section: Discussionmentioning

confidence: 99%

Enhanced proliferation in a prawn embryonic primary cell culture ectopically expressing mutated Ras

Sudarshan

Weil²,

Rotem-Dai³

et al. 2023

Front. Mar. Sci.

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“…The Parhyale genome has been sequenced and annotated (Kao et al 2016, see also Supplementary Materials) providing a valuable resource for transcriptomic studies. Finally, transgenic reporters and tools to manipulate gene function have been developed in this species, opening the way to functional genetic studies in the future (reviewed in Paris et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Distinct gene expression dynamics in developing and regenerating limbs

Sinigaglia

Almazán

Sémon

et al. 2021

Preprint

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Regenerating animals have the ability to reproduce organs that were originally generated 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.

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Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis

Sun¹,

Patel

2021

Preprint

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Emerging research organisms enable the study of biology that cannot be addressed using classical "model" organisms. The development of novel data resources can accelerate research in such animals. 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. Using a Minos transposase reporter system, we demonstrate the potential to identify novel regulatory elements using this approach, including distal regulatory elements. This work provides a platform for the identification of novel developmental regulatory elements in Parhyale, and offers a framework for performing such experiments in other emerging research organisms.

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The Crustacean Model <i>Parhyale hawaiensis</i>

Cited by 3 publications

References 107 publications

Enhanced proliferation in a prawn embryonic primary cell culture ectopically expressing mutated Ras

Enhanced proliferation in a prawn embryonic primary cell culture ectopically expressing mutated Ras

Distinct gene expression dynamics in developing and regenerating limbs

Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis

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