The crustacean model Parhyale hawaiensis

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

doi:10.1016/bs.ctdb.2022.02.001

Cited by 17 publications

(8 citation statements)

References 110 publications

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“…In this paper, we apply the Omni-ATAC-Seq protocol to embryos of the amphipod crustacean Parhyale hawaiensis, an emerging research organism for the study of arthropod development, evolution, and regeneration (Paris et al, 2021;Stamataki and Pavlopoulos, 2016;Sun and Patel, 2019). We identify dynamic regions of open chromatin ("peaks") across a broad swath of Parhyale developmental time.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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Emerging research organisms enable the study of biology that cannot be addressed using classical ‘model’ organisms. New 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 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 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. 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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Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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“…Small dry, clean weighing boat or petri dish Parhyale hawaiensis is a circumtropical marine amphipod crucial for epibenthic communities in tropical marine ecosystems (Poovachiranon et al, 1986). This amphipod has gained recognition for its sensitivity to environmental stressors and ecological signi cance, making it a promising model organism for tropical marine studies (Dos Santos et al, 2022) and a valuable laboratory model for various disciplines (Paris et al, 2022). To fully utilise P.…”

Section: Methodsmentioning

confidence: 99%

Assessing Growth Parameters in amphipod, Parhyale hawaiensis: Weighing and Measuring Length v1

Lawan

2024

Preprint

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“…Because of the increasing interest in the use of the marine amphipod Parhyale hawaiensis in ecotoxicology (Artal et al, 2018, 2019; Botelho et al, 2022; dos Santos, Botelho, et al, 2022; Dos Santos, Vannuci‐Silva, et al, 2022; Vacchi et al, 2019; Vannuci‐Silva et al, 2018, 2019) and in other sciences (Paris et al, 2022; Rehm et al, 2009), we here describe their hemocyte characteristics and identify the various cell types and their proportions, as well as their ability to phagocytize bacteria.…”

Section: Introductionmentioning

confidence: 99%

Characterization of hemocytes from the marine amphipod Parhyale hawaiensis (Dana 1853): Setting the basis for immunotoxicological studies

Santos

Botelho

Joviano

et al. 2023

Invertebrate Biology

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Hemocytes are circulating blood cells that play a crucial function in amphipods and other crustacean immune systems. The hemocytes of the marine tropical amphipod Parhyale hawaiensis have been used for the evaluation of DNA damage and micronuclei, but they have not been characterized in the scientific literature.The aim of this study was to describe the hemolymph cells of P. hawaiensis and study their phagocytotic activity. Basic dyes were used to differentiate the cell types and the presence of lipids. The total hemocyte counts (THCs) and the proportion and sizes of the hemocyte types were determined. Hemolymph was exposed to Escherichia coli for verification of the presence of phagocytosis. Three cell types, all containing lipids, were identified in P. hawaiensis: granulocytes (oval shape, 13.4 Â 7.6 μm), semi-granulocytes (oval shape, 14.1 Â 7.2 μm), and hyalinocytes (round shape, 9.6 Â 7.2 μm). Those three cell types were found in different percentages in males (64.8%, 31.1%, and 4.2%) and females (70.1%, 28.2%, and 1.7%). THCs for males were 9007 ± 3800 cells per individual and 4695 ± 1892 cells per individual for females. The cells of E. coli were phagocytized by the hemocytes. Our findings increased the knowledge of hemocytes in P. hawaiensis and is a step forward in using hemocyte-based immune responses as an endpoint in ecotoxicology.

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The crustacean model Parhyale hawaiensis

Cited by 17 publications

References 110 publications

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

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

Assessing Growth Parameters in amphipod, Parhyale hawaiensis: Weighing and Measuring Length v1

Characterization of hemocytes from the marine amphipod Parhyale hawaiensis (Dana 1853): Setting the basis for immunotoxicological studies

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