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Co-option of the PRDM14-CBFA2T complex from motor neurons to pluripotent cells during vertebrate evolution.

Latest Publications - Tue, 09/10/2019 - 12:34
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Co-option of the PRDM14-CBFA2T complex from motor neurons to pluripotent cells during vertebrate evolution.

Development. 2019 01 28;146(2):

Authors: Kawaguchi M, Sugiyama K, Matsubara K, Lin CY, Kuraku S, Hashimoto S, Suwa Y, Yong LW, Takino K, Higashida S, Kawamura D, Yu JK, Seki Y

Abstract
Gene regulatory networks underlying cellular pluripotency are controlled by a core circuitry of transcription factors in mammals, including POU5F1. However, the evolutionary origin and transformation of pluripotency-related transcriptional networks have not been elucidated in deuterostomes. PR domain-containing protein 14 (PRDM14) is specifically expressed in pluripotent cells and germ cells, and is required for establishing embryonic stem cells (ESCs) and primordial germ cells in mice. Here, we compared the functions and expression patterns of PRDM14 orthologues within deuterostomes. Amphioxus PRDM14 and zebrafish PRDM14, but not sea urchin PRDM14, compensated for mouse PRDM14 function in maintaining mouse ESC pluripotency. Interestingly, sea urchin PRDM14 together with sea urchin CBFA2T, an essential partner of PRDM14 in mouse ESCs, complemented the self-renewal defect in mouse Prdm14 KO ESCs. Contrary to the Prdm14 expression pattern in mouse embryos, Prdm14 was expressed in motor neurons of amphioxus embryos, as observed in zebrafish embryos. Thus, Prdm14 expression in motor neurons was conserved in non-tetrapod deuterostomes and the co-option of the PRDM14-CBFA2T complex from motor neurons into pluripotent cells may have maintained the transcriptional network for pluripotency during vertebrate evolution.This article has an associated 'The people behind the papers' interview.

PMID: 30630825 [PubMed - indexed for MEDLINE]

Categories: pubmed

Experiments reveal limited top-down control of key herbivores in southern California kelp forests.

Latest Publications - Tue, 09/03/2019 - 12:08
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Experiments reveal limited top-down control of key herbivores in southern California kelp forests.

Ecology. 2019 03;100(3):e02625

Authors: Dunn RP, Hovel KA

Abstract
Predator responses to gradients in prey density have important implications for population regulation and are a potential structuring force for subtidal marine communities, particularly on rocky reefs where herbivorous sea urchins can drive community state shifts. On rocky reefs in southern California where predatory sea otters have been extirpated, top-down control of sea urchins by alternative predators has been hypothesized but rarely tested experimentally. In laboratory feeding assays, predatory spiny lobsters (Panulirus interruptus) demonstrated a saturating functional response to urchin prey, whereby urchin proportional mortality was inversely density-dependent. In field experiments on rocky reefs near San Diego, California, predators (primarily the labrid fish California sheephead, Semicossyphus pulcher) inflicted highly variable mortality on purple urchin (Strongylocentrotus purpuratus) prey across all density levels. However, at low to moderate densities commonly observed within kelp forests, purple urchin mortality increased to a peak at a density of ~11 urchins/m2 . Above that level, at densities typical of urchin barrens, purple urchin mortality was density-independent. When larger red urchins (Mesocentrotus franciscanus) were offered to predators simultaneously with purple urchins, mortality was density-independent. Underwater videography revealed a positive relationship between purple urchin density and both the number and richness of fish predators, but these correlations were not observed when red urchins were present. Our results demonstrate highly variable mortality rates across prey densities in this system and suggest that top-down control of urchins can occur only under limited circumstances. Our findings provide insight into the dynamics of alternate community states observed on rocky reefs.

PMID: 30648729 [PubMed - indexed for MEDLINE]

Categories: pubmed

Transforming a transcription factor.

Latest Publications - Thu, 08/29/2019 - 12:03
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Transforming a transcription factor.

Elife. 2018 01 08;7:

Authors: Burke RD

Abstract
A transcription factor that regulates skeleton formation in sea urchin embryos has evolved a new domain that is essential for this process.

PMID: 29309030 [PubMed - indexed for MEDLINE]

Categories: pubmed

Toxicity of engineered micro- and nanomaterials with antifouling properties to the brine shrimp Artemia salina and embryonic stages of the sea urchin Paracentrotus lividus.

Latest Publications - Tue, 08/27/2019 - 12:02
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Toxicity of engineered micro- and nanomaterials with antifouling properties to the brine shrimp Artemia salina and embryonic stages of the sea urchin Paracentrotus lividus.

Environ Pollut. 2019 Aug;251:530-537

Authors: Gutner-Hoch E, Martins R, Maia F, Oliveira T, Shpigel M, Weis M, Tedim J, Benayahu Y

Abstract
Antifouling booster biocides are chemicals used in protective paints to tackle the adhesion of fouling organisms to maritime artificial structures. However, they are also known to exert toxic effects on non-target organisms. Recent research developments have highlighted the potential use of engineered micro/nanomaterials (EMNMs) as carriers of antifouling booster biocides in order to control their release and to reduce the harmful effects on living biota. In the present study, we sought to assess the toxicity of two commercially-available booster biocides: (zinc pyrithione (ZnPT) and copper pyrithione (CuPT)); three unloaded engineered micro/nanomaterials (EMNMs); layered double hydroxides (LDH), silica nanocapsules (SiNC), polyurea microcapsules (PU); , and six novel EMNMs (loaded with each of the two biocides). The exposure tests were conducted on the larval stage (nauplii) of the brine shrimp Artemia salina and on two embryonic developmental stages of the European purple sea urchin Paracentrotus lividus. The findings indicate that the unloaded LDH and PU (i.e. both biocide-free EMNMs) have non/low toxic effects on both species. The unloaded SiNC, in contrast, exerted a mild toxic effect on the A. salina nauplii and P. lividus embryos. The free biocides presented different toxicity values, with ZnPT being more toxic than CuPT in the P. lividus assays. LDH-based pyrithiones demonstrated lower toxicity compared to the free forms of the state-of-the-art compounds, and constitute good candidates in terms of their antifouling efficacy.

PMID: 31108285 [PubMed - indexed for MEDLINE]

Categories: pubmed

Exploring the Sea Urchin Neuropeptide Landscape by Mass Spectrometry.

Latest Publications - Wed, 08/21/2019 - 11:39
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Exploring the Sea Urchin Neuropeptide Landscape by Mass Spectrometry.

J Am Soc Mass Spectrom. 2018 05;29(5):923-934

Authors: Monroe EB, Annangudi SP, Wadhams AA, Richmond TA, Yang N, Southey BR, Romanova EV, Schoofs L, Baggerman G, Sweedler JV

Abstract
Neuropeptides are essential cell-to-cell signaling messengers and serve important regulatory roles in animals. Although remarkable progress has been made in peptide identification across the Metazoa, for some phyla such as Echinodermata, limited neuropeptides are known and even fewer have been verified on the protein level. We employed peptidomic approaches using bioinformatics and mass spectrometry (MS) to experimentally confirm 23 prohormones and to characterize a new prohormone in nervous system tissue from Strongylocentrotus purpuratus, the purple sea urchin. Ninety-three distinct peptides from known and novel prohormones were detected with MS from extracts of the radial nerves, many of which are reported or experimentally confirmed here for the first time, representing a large-scale study of neuropeptides from the phylum Echinodermata. Many of the identified peptides and their precursor proteins have low homology to known prohormones from other species/phyla and are unique to the sea urchin. By pairing bioinformatics with MS, the capacity to characterize novel peptides and annotate prohormone genes is enhanced. Graphical Abstract.

PMID: 29667164 [PubMed - indexed for MEDLINE]

Categories: pubmed

Growth of second stage mineral in Lytechinus variegatus.

Latest Publications - Sat, 08/10/2019 - 11:08
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Growth of second stage mineral in Lytechinus variegatus.

Connect Tissue Res. 2018 07;59(4):345-355

Authors: Stock SR, Seto J, Deymier AC, Rack A, Veis A

Abstract
Purpose and Aims: Sea urchin teeth consist of calcite and form in two stages with different magnesium contents. The first stage structures of independently formed plates and needle-prisms define the shape of the tooth, and the columns of the second stage mineral cements the first stage structures together and control the fracture behavior of the mature tooth. This study investigates the nucleation and growth of the second stage mineral.
MATERIALS AND METHODS: Scanning electron microscopy (SEM) and synchrotron microComputed Tomography characterized the structures of the second phase material found in developing of Lytechinus variegatus teeth.
RESULTS: Although the column development is a continuous process, defining four phases of column formation captures the changes that occur in teeth of L. variegatus. The earliest phase consists of small 1-2 µm diameter hemispheres, and the second of 5-10 µm diameter, mound-like structures with a nodular surface, develops from the hemispheres. The mounds eventually bridge the syncytium between adjacent plates and form hyperboloid structures (phase three) that appear like mesas when plates separate during the fracture. The mesa diameter increases with time until the column diameter is significantly larger than its height, defining the fourth phase of column development. Energy dispersive x-ray spectroscopy confirms that the columns contain more magnesium than the underlying plates; the ratios of magnesium to calcium are consistent with compositions derived from x-ray diffraction.
CONCLUSION: Columns grow from both bounding plates. The presence of first phase columns interspersed among third stage mesas indicates very localized control of mineralization.

PMID: 29083939 [PubMed - indexed for MEDLINE]

Categories: pubmed

Electron microscopic characterization of nuclear egress in the sea urchin gastrula.

Latest Publications - Fri, 08/09/2019 - 11:08
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Electron microscopic characterization of nuclear egress in the sea urchin gastrula.

J Morphol. 2018 05;279(5):609-615

Authors: LaMassa N, Arenas-Mena C, Phillips GR

Abstract
Nuclear egress, also referred to as nuclear envelope (NE) budding, is a process of transport in which vesicles containing molecular complexes or viral particles leave the nucleus through budding from the inner nuclear membrane (INM) to enter the perinuclear space. Following this event, the perinuclear vesicles (PNVs) fuse with the outer nuclear membrane (ONM), where they release their contents into the cytoplasm. Nuclear egress is thought to participate in many functions such as viral replication, cellular differentiation, and synaptic development. The molecular basis for nuclear egress is now beginning to be elucidated. Here, we observe in the sea urchin gastrula, using serial section transmission electron microscopy, strikingly abundant PNVs containing as yet unidentified granules that resemble the ribonucleoprotein complexes (RNPs) previously observed in similar types of PNVs. Some PNVs were observed in the process of fusion with the ONM where they appeared to release their contents into the cytoplasm. These vesicles were abundantly observed in all three presumptive germ layers. These findings indicate that nuclear egress is likely to be an important mechanism for nucleocytoplasmic transfer during sea urchin development. The sea urchin may be a useful model to characterize further and gain a better understanding of the process of nuclear egress.

PMID: 29383750 [PubMed - indexed for MEDLINE]

Categories: pubmed

Sea Urchin Embryo Model As a Reliable in Vivo Phenotypic Screen to Characterize Selective Antimitotic Molecules. Comparative evaluation of Combretapyrazoles, -isoxazoles, -1,2,3-triazoles, and -pyrroles as Tubulin-Binding Agents.

Latest Publications - Fri, 08/02/2019 - 10:46
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Sea Urchin Embryo Model As a Reliable in Vivo Phenotypic Screen to Characterize Selective Antimitotic Molecules. Comparative evaluation of Combretapyrazoles, -isoxazoles, -1,2,3-triazoles, and -pyrroles as Tubulin-Binding Agents.

ACS Comb Sci. 2018 12 10;20(12):700-721

Authors: Semenova MN, Demchuk DV, Tsyganov DV, Chernysheva NB, Samet AV, Silyanova EA, Kislyi VP, Maksimenko AS, Varakutin AE, Konyushkin LD, Raihstat MM, Kiselyov AS, Semenov VV

Abstract
A series of both novel and reported combretastatin analogues, including diarylpyrazoles, -isoxazoles, -1,2,3-triazoles, and -pyrroles, were synthesized via improved protocols to evaluate their antimitotic antitubulin activity using in vivo sea urchin embryo assay and a panel of human cancer cells. A systematic comparative structure-activity relationship studies of these compounds were conducted. Pyrazoles 1i and 1p, isoxazole 3a, and triazole 7b were found to be the most potent antimitotics across all tested compounds causing cleavage alteration of the sea urchin embryo at 1, 0.25, 1, and 0.5 nM, respectively. These agents exhibited comparable cytotoxicity against human cancer cells. Structure-activity relationship studies revealed that compounds substituted with 3,4,5-trimethoxyphenyl ring A and 4-methoxyphenyl ring B displayed the highest activity. 3-Hydroxy group in the ring B was essential for the antiproliferative activity in the diarylisoxazole series, whereas it was not required for potency of diarylpyrazoles. Isoxazoles 3 with 3,4,5-trimethoxy-substituted ring A and 3-hydroxy-4-methoxy-substituted ring B were more active than the respective pyrazoles 1. Of the azoles substituted with the same set of other aryl pharmacophores, diarylpyrazoles 1, 4,5-diarylisoxazoles 3, and 4,5-diaryl-1,2,3-triazoles 7 displayed similar strongest antimitotic antitubulin effect followed by 3,4-diarylisoxazoles 5, 1,5-diaryl-1,2,3-triazoles 8, and pyrroles 10 that showed the lowest activity. Introduction of the amino group into the heterocyclic core decreased the antimitotic antitubulin effect of pyrazoles, triazoles, and to a lesser degree of 4,5-diarylisoxazoles, whereas potency of the respective 3,4-diarylisoxazoles was increased.

PMID: 30452225 [PubMed - indexed for MEDLINE]

Categories: pubmed

Methods for the experimental and computational analysis of gene regulatory networks in sea urchins.

Latest Publications - Fri, 07/26/2019 - 10:36
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Methods for the experimental and computational analysis of gene regulatory networks in sea urchins.

Methods Cell Biol. 2019;151:89-113

Authors: Peter IS

Abstract
The discovery of gene regulatory networks (GRNs) has opened a gate to access the genomic mechanisms controlling development. GRNs are systems of transcriptional regulatory circuits that control the differential specification of cell fates during development by regulating gene expression. The experimental analysis of GRNs involves a collection of methods, each revealing aspects of the overall control process. This review provides an overview of experimental and computational methods that have been successfully applied for solving developmental GRNs in the sea urchin embryo. The key in this approach is to obtain experimental evidence for functional interactions between transcription factors and regulatory DNA. In the second part of this review, a more generally applicable strategy is discussed that shows a path from experimental evidence to annotation of regulatory linkages to the generation of GRN models.

PMID: 30948033 [PubMed - indexed for MEDLINE]

Categories: pubmed

The causes of things.

Latest Publications - Fri, 07/26/2019 - 10:36
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The causes of things.

Methods Cell Biol. 2019;151:49-54

Authors: Burke RD

Abstract
Studies using sea urchins have contributed substantially to our understanding of how a fertilized egg is transformed during embryonic development. This brief review provides a personal perspective of the remarkable advances that have occurred over the past 45 years in our understanding of how urchin embryos work.

PMID: 30948029 [PubMed - indexed for MEDLINE]

Categories: pubmed

Probing Ca2+ release mechanisms using sea urchin egg homogenates.

Latest Publications - Fri, 07/26/2019 - 10:36
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Probing Ca2+ release mechanisms using sea urchin egg homogenates.

Methods Cell Biol. 2019;151:445-458

Authors: Yuan Y, Gunaratne GS, Marchant JS, Patel S

Abstract
Sea urchin eggs have been extensively used to study Ca2+ release through intracellular Ca2+-permeable channels. Their amenability to homogenization yields a robust, cell-free preparation that was central to establishing the Ca2+ mobilizing actions of cyclic ADP-ribose and NAADP. Egg homogenates have continued to provide insight into the basic properties and pharmacology of intracellular Ca2+ release channels. In this chapter, we describe methods for the preparation of egg homogenates and monitoring Ca2+ release using fluorimetry and radiotracer flux.

PMID: 30948025 [PubMed - indexed for MEDLINE]

Categories: pubmed

Spatially mapping gene expression in sea urchin primary mesenchyme cells.

Latest Publications - Fri, 07/26/2019 - 10:36
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Spatially mapping gene expression in sea urchin primary mesenchyme cells.

Methods Cell Biol. 2019;151:433-442

Authors: Zuch DT, Bradham CA

Abstract
During sea urchin embryogenesis, primary mesenchyme cells (PMCs) follow a stereotypical migratory program, arrange into a primary pattern, then begin to secrete a bilaterally symmetric calcium carbonate skeleton. Recently identified genes are expressed in spatially-restricted domains within the PMC population (Sun & Ettensohn, 2014). To better understand the molecular mechanisms orchestrating PMC positioning, we are characterizing the expression profiles of PMC subset-specific genes. To deconvolve the spatiotemporal expression patterns within PMCs, we detect cell-specific mRNA expression with combined RNA fluorescence in situ hybridization and immunolabeling of PMCs. Subsequent confocal microscopy provides 3D position and expression information for individual PMCs. We extract PMC positions and relative gene expression levels, then model these results using open-source 3D modeling software. This versatile protocol can be extended to other models and systems.

PMID: 30948024 [PubMed - indexed for MEDLINE]

Categories: pubmed

From hemoglobin to urchin spicules.

Latest Publications - Fri, 07/26/2019 - 10:36
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From hemoglobin to urchin spicules.

Methods Cell Biol. 2019;151:43-45

Authors: Wilt F

Abstract
A retrospective of an academic career. The article poses the question about the values involved in a life in the academy, starting with the role of hemoglobin in the chick embryo and ending with the role of calcium in the sea urchin spine.

PMID: 30948023 [PubMed - indexed for MEDLINE]

Categories: pubmed

Echinoderm eggs as a model for discoveries in cell biology.

Latest Publications - Fri, 07/26/2019 - 10:36
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Echinoderm eggs as a model for discoveries in cell biology.

Methods Cell Biol. 2019;151:29-36

Authors: Burgess DR

Abstract
I happen to have been trained in cell and developmental biology in the early 1970s, which was near the beginning of the explosive growth of the field of cell biology. The American Society for Cell Biology had been founded in 1960 and so the field was in its early days. Cell biology research was dominated by the use of the electron microscope and by protein biochemistry. Molecular biology and the use of genetics were in their infancy. When we track the path of discoveries in cell biology contributed by research using echinoderm eggs, we follow the development of new technologies in genetics, molecular biology, biochemistry and biophysics, bioengineering, and imaging. The changes in approaches and methods have led to many key discoveries in cell biology through the use of sea urchin, sand dollar and sea star eggs. These include the discovery of cyclin, cytoplasmic dynein, rho activation for cytokinesis, new membrane addition as a late event in cytokinesis, multiple kinesins playing multiple roles, how flagella beat, the dynamics of microtubules in the mitotic apparatus, control over centrosomes and cell cycle checkpoints, the process of nuclear envelope breakdown for cell division, the discovery of 1-methyl adenine (hormones) as the trigger for meiotic maturation, Ca++ transients controlling cell activation and exocytosis among others. What I hope to provide in this perspective is to highlight some of those wonderful discoveries as my own career evolved to contribute to the field.

PMID: 30948013 [PubMed - indexed for MEDLINE]

Categories: pubmed

Trapping, tagging and tracking: Tools for the study of proteins during early development of the sea urchin.

Latest Publications - Fri, 07/26/2019 - 10:36
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Trapping, tagging and tracking: Tools for the study of proteins during early development of the sea urchin.

Methods Cell Biol. 2019;151:283-304

Authors: Roux-Osovitz MM, Foltz KR, Oulhen N, Wessel G

Abstract
The exquisite synchronicity of sea urchin development provides a reliable model for studying maternal proteins in the haploid egg as well as those involved in egg activation, fertilization and early development. Sea urchin eggs are released by the millions, enabling the quantitative evaluation of maternally stored and newly synthesized proteins over a range of time (seconds to hours post fertilization). During this window of development exist many hallmark and unique biochemical interactions that can be investigated for the purpose of characterizing profiles of kinases and other signaling proteins, manipulated using pharmacology to test sufficiency and necessity, for identification of post translational modifications, and for capturing protein-protein interactions. Coupled with the fact that sea urchin eggs and embryos are transparent, this synchronicity also results in large populations of cells that can be evaluated for newly synthesized protein localization and identification through use of the Click-iT technology. We provide basic protocols for these approaches and direct readers to the appropriate literature for variations and examples.

PMID: 30948012 [PubMed - indexed for MEDLINE]

Categories: pubmed

Whole mount in situ hybridization techniques for analysis of the spatial distribution of mRNAs in sea urchin embryos and early larvae.

Latest Publications - Fri, 07/26/2019 - 10:36
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Whole mount in situ hybridization techniques for analysis of the spatial distribution of mRNAs in sea urchin embryos and early larvae.

Methods Cell Biol. 2019;151:177-196

Authors: Erkenbrack EM, Croce JC, Miranda E, Gautam S, Martinez-Bartolome M, Yaguchi S, Range RC

Abstract
A critical process in embryonic development is the activation and spatial localization of mRNAs to specific cells and territories of the embryo. Revealing the spatial distribution of mRNAs and how it changes during development is a vital piece of information that aids in understanding the signaling and regulatory genes driving specific gene regulatory networks. In the laboratory, a cost-efficient, reliable method to determine the spatial distribution of mRNAs in embryos is in situ hybridization. This sensitive and straightforward method employs exogenous antisense RNA probes to find specific and complementary sequences in fixed embryos. Antigenic moieties conjugated to the ribonucleotides incorporated in the probe cross-react with antibodies, and numerous staining methods can be subsequently employed to reveal the spatial distribution of the targeted mRNA. The quality of the data produced by this method is equivalent to the experience of the researcher, and thus a thorough understanding of the numerous steps comprising this method is important for obtaining high quality data. Here we compile and summarize several protocols that have been employed chiefly on five sea urchin species in numerous laboratories around the world. Whereas the protocols can vary for the different species, the overarching steps are similar and can be readily mastered. When properly and carefully undertaken, in situ hybridization is a powerful tool providing unambiguous data for which there currently is no comparable substitute and will continue to be an important method in the era of big data and beyond.

PMID: 30948007 [PubMed - indexed for MEDLINE]

Categories: pubmed

Multiplex cis-regulatory analysis.

Latest Publications - Fri, 07/26/2019 - 10:36
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Multiplex cis-regulatory analysis.

Methods Cell Biol. 2019;151:159-176

Authors: Nam J

Abstract
Recent progress in multiplex cis-regulatory analysis has increased the speed of identifying enhancers and promoters, and enabled efficient incorporation of cis-regulatory information into gene regulatory network models. Three types of barcode reporters have been developed for multiplex reporter assays in sea urchin embryos: 13-tags and 129-tags for QPCR, 130 Nanotags for NanoString, and 100 million N25-tags for next-generation sequencing. In this chapter, to facilitate adoption of high-throughput cis-regulatory analysis in sea urchin embryos, I provide practical guidelines to best utilize barcode reporters that are compatible with either QPCR or next-generation sequencing. I expect that the guidelines are also applicable to other invertebrate embryos.

PMID: 30948006 [PubMed - indexed for MEDLINE]

Categories: pubmed

Interactive effects of predator and prey harvest on ecological resilience of rocky reefs.

Latest Publications - Wed, 07/24/2019 - 21:43
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Interactive effects of predator and prey harvest on ecological resilience of rocky reefs.

Ecol Appl. 2017 09;27(6):1718-1730

Authors: Dunn RP, Baskett ML, Hovel KA

Abstract
A major goal of ecosystem-based fisheries management is to prevent fishery-induced shifts in community states. This requires an understanding of ecological resilience: the ability of an ecosystem to return to the same state following a perturbation, which can strongly depend on species interactions across trophic levels. We use a structured model of a temperate rocky reef to explore how multi-trophic level fisheries impact ecological resilience. Increasing fishing mortality of prey (urchins) has a minor effect on equilibrium biomass of kelp, urchins, and spiny lobster predators, but increases resilience by reducing the range of predator harvest rates at which alternative stable states are possible. Size-structured predation on urchins acts as the feedback maintaining each state. Our results demonstrate that the resilience of ecosystems strongly depends on the interactive effects of predator and prey harvest in multi-trophic level fisheries, which are common in marine ecosystems but are unaccounted for by traditional management.

PMID: 28581670 [PubMed - indexed for MEDLINE]

Categories: pubmed