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De Rinaldis G, Leone A, De Domenico S, Bosch-Belmar M, Slizyte R, Milisenda G, Santucci A, Albano C, Piraino S. Biochemical Characterization of Cassiopea andromeda (Forsskål, 1775), Another Red Sea Jellyfish in the Western Mediterranean Sea. Mar Drugs 2021; 19:md19090498. [PMID: 34564160 PMCID: PMC8472248 DOI: 10.3390/md19090498] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 11/16/2022] Open
Abstract
Increasing frequency of native jellyfish proliferations and massive appearance of non-indigenous jellyfish species recently concur to impact Mediterranean coastal ecosystems and human activities at sea. Nonetheless, jellyfish biomass may represent an exploitable novel resource to coastal communities, with reference to its potential use in the pharmaceutical, nutritional, and nutraceutical Blue Growth sectors. The zooxanthellate jellyfish Cassiopea andromeda, Forsskål, 1775 (Cnidaria, Rhizostomeae) entered the Levant Sea through the Suez Canal and spread towards the Western Mediterranean to reach Malta, Tunisia, and recently also the Italian coasts. Here we report on the biochemical characterization and antioxidant activity of C. andromeda specimens with a discussion on their relative biological activities. The biochemical characterization of the aqueous (PBS) and hydroalcoholic (80% ethanol) soluble components of C. andromeda were performed for whole jellyfish, as well as separately for umbrella and oral arms. The insoluble components were hydrolyzed by sequential enzymatic digestion with pepsin and collagenase. The composition and antioxidant activity of the insoluble and enzymatically digestible fractions were not affected by the pre-extraction types, resulting into collagen- and non-collagen-derived peptides with antioxidant activity. Both soluble compounds and hydrolyzed fractions were characterized for the content of proteins, phenolic compounds, and lipids. The presence of compounds coming from the endosymbiont zooxanthellae was also detected. The notable yield and the considerable antioxidant activity detected make this species worthy of further study for its potential biotechnological sustainable exploitation.
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Affiliation(s)
- Gianluca De Rinaldis
- Institute of Sciences of Food Production (CNR-ISPA, Unit of Lecce), National Research Council, Via Monteroni, 73100 Lecce, Italy; (G.D.R.); (S.D.D.); (C.A.)
- Department of Biotechnology Chemistry and Pharmacy (DBCF), Università Degli Studi Di Siena, Via A. Moro, 53100 Siena, Italy;
| | - Antonella Leone
- Institute of Sciences of Food Production (CNR-ISPA, Unit of Lecce), National Research Council, Via Monteroni, 73100 Lecce, Italy; (G.D.R.); (S.D.D.); (C.A.)
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa, Local Unit of Lecce), Via Monteroni, 73100 Lecce, Italy;
- Correspondence: ; Tel.: +39-0832-422615
| | - Stefania De Domenico
- Institute of Sciences of Food Production (CNR-ISPA, Unit of Lecce), National Research Council, Via Monteroni, 73100 Lecce, Italy; (G.D.R.); (S.D.D.); (C.A.)
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Campus Ecotekne, University of Salento, Via Lecce-Monteroni, 73100 Lecce, Italy
| | - Mar Bosch-Belmar
- Laboratory of Ecology, Department of Earth and Marine Sciences (DiSTeM), University of Palermo, 90128 Palermo, Italy;
| | - Rasa Slizyte
- Department of Fisheries and New Biomarine Industry, SINTEF Ocean, Brattørkaia 17C, 7010 Trondheim, Norway;
| | - Giacomo Milisenda
- Centro Interdipartimentale della Sicilia, Stazione Zoologica Anton Dohrn, Lungomare Cristoforo Colombo, 90142 Palermo, Italy;
| | - Annalisa Santucci
- Department of Biotechnology Chemistry and Pharmacy (DBCF), Università Degli Studi Di Siena, Via A. Moro, 53100 Siena, Italy;
| | - Clara Albano
- Institute of Sciences of Food Production (CNR-ISPA, Unit of Lecce), National Research Council, Via Monteroni, 73100 Lecce, Italy; (G.D.R.); (S.D.D.); (C.A.)
| | - Stefano Piraino
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa, Local Unit of Lecce), Via Monteroni, 73100 Lecce, Italy;
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Campus Ecotekne, University of Salento, Via Lecce-Monteroni, 73100 Lecce, Italy
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Senter DM, Douglas DR, Strickland WC, Thomas SG, Talkington AM, Miller LA, Battista NA. A semi-automated finite difference mesh creation method for use with immersed boundary software IB2d and IBAMR. BIOINSPIRATION & BIOMIMETICS 2020; 16:10.1088/1748-3190/ababb0. [PMID: 32746437 PMCID: PMC7970534 DOI: 10.1088/1748-3190/ababb0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Numerous fluid-structure interaction problems in biology have been investigated using the immersed boundary method. The advantage of this method is that complex geometries, e.g., internal or external morphology, can easily be handled without the need to generate matching grids for both the fluid and the structure. Consequently, the difficulty of modeling the structure lies often in discretizing the boundary of the complex geometry (morphology). Both commercial and open source mesh generators for finite element methods have long been established; however, the traditional immersed boundary method is based on a finite difference discretization of the structure. Here we present a software library for obtaining finite difference discretizations of boundaries for direct use in the 2D immersed boundary method. This library provides tools for extracting such boundaries as discrete mesh points from digital images. We give several examples of how the method can be applied that include passing flow through the veins of insect wings, within lymphatic capillaries, and around starfish using open-source immersed boundary software.
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Affiliation(s)
- D Michael Senter
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
- Bioinformatics. and Comp. Biology, CB 7264, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States of America
| | - Dylan R Douglas
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
- Department of Mathematics, University of Arizona, 617 N. Santa Rita Ave. P.O. Box 210089 Tucson, AZ 85721-0089, United States of America
| | - W Christopher Strickland
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
- Dept. of Mathematics, 1403 Circle Drive, University of Tennessee at Knoxville, Knoxville, TN 37919, United States of America
| | - Steven G Thomas
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
| | - Anne M Talkington
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
- Bioinformatics. and Comp. Biology, CB 7264, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States of America
| | - Laura A Miller
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
- Bioinformatics. and Comp. Biology, CB 7264, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States of America
- Department of Mathematics, University of Arizona, 617 N. Santa Rita Ave. P.O. Box 210089 Tucson, AZ 85721-0089, United States of America
| | - Nicholas A Battista
- Dept. of Mathematics and Statistics, The College of New Jersey, 2000 Pennington Rd., Ewing, NJ 08628, United States of America
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Alben S, Puritz C. Intermittent sliding locomotion of a two-link body. Phys Rev E 2020; 101:052613. [PMID: 32575270 DOI: 10.1103/physreve.101.052613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/07/2020] [Indexed: 11/07/2022]
Abstract
We study the possibility of efficient intermittent locomotion for two-link bodies that slide by changing their interlink angle periodically in time. We find that the anisotropy ratio of the sliding friction coefficients is a key parameter, while solutions have a simple scaling dependence on the friction coefficients' magnitudes. With very anisotropic friction, efficient motions involve coasting in low-drag states, with rapid and asymmetric power and recovery strokes. As the anisotropy decreases, burst-and-coast motions change to motions with long power strokes and short recovery strokes, and roughly constant interlink angle velocity on each. These motions are seen in the spaces of sinusoidal and power-law motions described by two and five parameters, respectively. Allowing the duty cycle to vary greatly increases the motions' efficiency compared to the case of symmetric power and recovery strokes. Allowing further variations in the concavity of the power and recovery strokes improves the efficiency further only when friction is very anisotropic. Near isotropic friction, a variety of optimally efficient motions are found with more complex waveforms. Many of the optimal sinusoidal and power-law motions are similar to those that we find with an optimization search in the space of more general periodic functions (truncated Fourier series). When we increase the resistive force's power-law dependence on velocity, the optimal motions become smoother, slower, and less efficient, particularly near isotropic friction.
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Affiliation(s)
- Silas Alben
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Connor Puritz
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan 48109, USA
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Naut Your Everyday Jellyfish Model: Exploring How Tentacles and Oral Arms Impact Locomotion. FLUIDS 2019. [DOI: 10.3390/fluids4030169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Jellyfish are majestic, energy-efficient, and one of the oldest species that inhabit the oceans. It is perhaps the second item, their efficiency, that has captivated scientists for decades into investigating their locomotive behavior. Yet, no one has specifically explored the role that their tentacles and oral arms may have on their potential swimming performance. We perform comparative in silico experiments to study how tentacle/oral arm number, length, placement, and density affect forward swimming speeds, cost of transport, and fluid mixing. An open source implementation of the immersed boundary method was used (IB2d) to solve the fully coupled fluid–structure interaction problem of an idealized flexible jellyfish bell with poroelastic tentacles/oral arms in a viscous, incompressible fluid. Overall tentacles/oral arms inhibit forward swimming speeds, by appearing to suppress vortex formation. Nonlinear relationships between length and fluid scale (Reynolds Number) as well as tentacle/oral arm number, density, and placement are observed, illustrating that small changes in morphology could result in significant decreases in swimming speeds, in some cases by upwards of 80–90% between cases with or without tentacles/oral arms.
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Ohdera AH, Abrams MJ, Ames CL, Baker DM, Suescún-Bolívar LP, Collins AG, Freeman CJ, Gamero-Mora E, Goulet TL, Hofmann DK, Jaimes-Becerra A, Long PF, Marques AC, Miller LA, Mydlarz LD, Morandini AC, Newkirk CR, Putri SP, Samson JE, Stampar SN, Steinworth B, Templeman M, Thomé PE, Vlok M, Woodley CM, Wong JC, Martindale MQ, Fitt WK, Medina M. Upside-Down but Headed in the Right Direction: Review of the Highly Versatile Cassiopea xamachana System. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00035] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Battista NA, Strickland WC, Miller LA. IB2d: a Python and MATLAB implementation of the immersed boundary method. BIOINSPIRATION & BIOMIMETICS 2017; 12:036003. [PMID: 28355146 PMCID: PMC7970532 DOI: 10.1088/1748-3190/aa5e08] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The development of fluid-structure interaction (FSI) software involves trade-offs between ease of use, generality, performance, and cost. Typically there are large learning curves when using low-level software to model the interaction of an elastic structure immersed in a uniform density fluid. Many existing codes are not publicly available, and the commercial software that exists usually requires expensive licenses and may not be as robust or allow the necessary flexibility that in house codes can provide. We present an open source immersed boundary software package, IB2d, with full implementations in both MATLAB and Python, that is capable of running a vast range of biomechanics models and is accessible to scientists who have experience in high-level programming environments. IB2d contains multiple options for constructing material properties of the fiber structure, as well as the advection-diffusion of a chemical gradient, muscle mechanics models, and artificial forcing to drive boundaries with a preferred motion.
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Affiliation(s)
- Nicholas A Battista
- Department of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America. Department of Biology, CB 3280, University of North Carolina, Chapel Hill, NC, 27599, United States of America. www.github.com/nickabattista/IB2d
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