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Colin S.P.,Roger Williams University | Colin S.P.,Whitman Center | Costello J.H.,Whitman Center | Costello J.H.,Providence College | And 3 more authors.
PLoS ONE | Year: 2013

Evolutionary constraints which limit the forces produced during bell contractions of medusae affect the overall medusan morphospace such that jet propulsion is limited to only small medusae. Cubomedusae, which often possess large prolate bells and are thought to swim via jet propulsion, appear to violate the theoretical constraints which determine the medusan morphospace. To examine propulsion by cubomedusae, we quantified size related changes in wake dynamics, bell shape, swimming and turning kinematics of two species of cubomedusae, Chironex fleckeri and Chiropsella bronzie. During growth, these cubomedusae transitioned from using jet propulsion at smaller sizes to a rowing-jetting hybrid mode of propulsion at larger sizes. Simple modifications in the flexibility and kinematics of their velarium appeared to be sufficient to alter their propulsive mode. Turning occurs during both bell contraction and expansion and is achieved by generating asymmetric vortex structures during both stages of the swimming cycle. Swimming characteristics were considered in conjunction with the unique foraging strategy used by cubomedusae. © 2013 Colin et al.


News Article | December 27, 2016
Site: www.eurekalert.org

WOODS HOLE, MASS. -- One of the most profound changes in the life of an organism is what Antonio Giraldez calls "embryonic puberty": the stage when an early embryo stops taking instructions from its mother on how to develop and activates its own genome to kick out those instructions instead. This critical stage, called the maternal-to-zygote transition, happens in all embryos, from sea anemones to humans. Yet how it is regulated in the embryo is not yet known. This week in Nature Methods, Giraldez and colleagues present a novel way to decipher the genetic code that embryos use to instruct many maternal messages (mRNAs) to be destroyed, and others to become stabilized. Giraldez is a Professor of Genetics at Yale University School of Medicine and was a 2016 Research Awardee in the MBL Whitman Center, where he conducted part of this research. The method, called RESA (RNA Element Selection Assay), has broad applications, Giraldez says. "It's a modular method we can use in many contexts, depending on the question the investigator wants to ask, to dissect the meaning of different parts of the genome. It is a molecular 'Rosetta stone' to help us decode the functional elements within the genome." In this case, they used RESA to detect the stability or decay of millions of RNA fragments in the zebrafish embryo, which in turn gave information about the genes that are shut down or activated during the maternal-to-zygote transition. The team developed RESA in zebrafish, Giraldez says, "but the goal is to use it across many different species, so we can find meaningful 'words' or instructions in the genome from squid to mouse to human." He plans to continue testing RESA in squid and other marine model systems at the MBL next year, such as sea urchin and ctenophores. "That's the part I am most excited about, is the MBL offers us this opportunity to test RESA across many species," Giraldez says. "That is priceless; it's work that cannot be done anywhere else in the world." "The MBL made me realize that we know so much about a few species, and so little about so many other species," Giraldez says. "But now, with new sequencing technologies like RESA, we can really understand biology much more broadly across species. That is really a new revolution." The Marine Biological Laboratory (MBL) is dedicated to scientific discovery - exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.


News Article | April 28, 2016
Site: phys.org

"Cells adopt diverse shapes that are related to how they function. We wondered if cells have the ability to perceive their own shapes, specifically, the curvature of the [cell] membrane," says Drew Bridges, a Ph.D. candidate in the laboratory of Amy Gladfelter, associate professor of biological sciences at Dartmouth College and a scientist in the MBL's Whitman Center. The team focused on the septins, proteins that are usually found near micron-scaled curves in the cell membrane, such as the furrow that marks where the cell will pinch together and divide. Using live-cell imaging at the MBL, they noticed that septins in a novel model system, the fungus Ashbya gossypii, tended to congregate on fungus branches where curvature was highest. They then decided to recreate this natural phenomenon in the lab, using artificial materials they could measure more easily than living cells. Using precisely scaled glass beads coated with lipid membranes, they discovered that septin proteins preferred curves in the 1-3 micron range. They got the same result using human or fungal septins, suggesting that this phenomenon is evolutionarily conserved. "This ability of septins to sense micron-scaled cell curvature provides cells with a previously unknown mechanism for organizing themselves," Bridges says. The idea for the glass bead experiment came from "many rich intellectual discussions with other members of the MBL community," says Bridges, who has accompanied Gladfelter to the MBL each summer since 2012. "Both our collaborations and the imaging resources at MBL were central to this work." More information: Andrew A. Bridges et al, Micron-scale plasma membrane curvature is recognized by the septin cytoskeleton, The Journal of Cell Biology (2016). DOI: 10.1083/jcb.201512029


News Article | April 20, 2016
Site: www.biosciencetechnology.com

Sharks, skates, and rays are oddities among the fish: They have appendages growing out of the gill arch, a small cradle of bones that supports the gills. This anatomical peculiarity has led to the proposal that the paired limbs of humans, and before that the paired fins of fish, evolved from the transformation of gill arches in early fish. Genetic evidence for this theory is offered in a new study led by J. Andrew Gillis, a Royal Society University Research Fellow at the University of Cambridge, U.K., and a Whitman Center scientist at the Marine Biological Laboratory (MBL) in Woods Hole, Mass. The study, published this week in Development, demonstrates striking similarities in the genetic mechanism used to pattern gill arch appendages (called branchial rays) and fins/limbs. Studying embryos of the little skate, Gillis focused on the gene Sonic hedgehog, which produces a signaling protein whose function is well understood in the mammalian limb. Remarkably, he found that Sonic hedgehog's role in branchial rays closely parallels its role in the limb: it sets up the axis of development and, later, maintains growth of the limb skeleton. "The shared role of Sonic hedgehog in patterning branchial rays and limbs may be due to a deep evolutionary relationship between the two," Gillis says, "or it may simply be that two unrelated appendages independently use the same gene for the same function." Ongoing studies comparing the function of other genes during branchial ray and fin/limb development will help to resolve this. Gillis will continue his research at the MBL this summer using skates collected and supplied by the Marine Resources Department. "Branchial rays will figure prominently in the story of the evolutionary origin of vertebrate animal appendages, either by shedding light on the evolutionary antecedent of paired fins/limbs, or by teaching us about the genetic mechanisms that animals can use to invent new appendages," Gillis says.


News Article | December 27, 2016
Site: phys.org

Zebrafish embryo superimposed with a 'Rosetta Stone' that reads: 'This paper identifies regulatory sequences in RNA by analyzing their regulatory function in a massive parallel reporter assay during embryogenesis. The method is called RESA and stands for RNA Element Selection Assay.' Credit: Antonio Giraldez One of the most profound changes in the life of an organism is what Antonio Giraldez calls "embryonic puberty": the stage when an early embryo stops taking instructions from its mother on how to develop and activates its own genome to kick out those instructions instead. This critical stage, called the maternal-to-zygote transition, happens in all embryos, from sea anemones to humans. Yet how it is regulated in the embryo is not yet known. This week in Nature Methods, Giraldez and colleagues present a novel way to decipher the genetic code that embryos use to instruct many maternal messages (mRNAs) to be destroyed, and others to become stabilized. Giraldez is a Professor of Genetics at Yale University School of Medicine and was a 2016 Research Awardee in the MBL Whitman Center, where he conducted part of this research. The method, called RESA (RNA Element Selection Assay), has broad applications, Giraldez says. "It's a modular method we can use in many contexts, depending on the question the investigator wants to ask, to dissect the meaning of different parts of the genome. It is a molecular 'Rosetta stone' to help us decode the functional elements within the genome." In this case, they used RESA to detect the stability or decay of millions of RNA fragments in the zebrafish embryo, which in turn gave information about the genes that are shut down or activated during the maternal-to-zygote transition. The team developed RESA in zebrafish, Giraldez says, "but the goal is to use it across many different species, so we can find meaningful 'words' or instructions in the genome from squid to mouse to human." He plans to continue testing RESA in squid and other marine model systems at the MBL next year, such as sea urchin and ctenophores. "That's the part I am most excited about, is the MBL offers us this opportunity to test RESA across many species," Giraldez says. "That is priceless; it's work that cannot be done anywhere else in the world." "The MBL made me realize that we know so much about a few species, and so little about so many other species," Giraldez says. "But now, with new sequencing technologies like RESA, we can really understand biology much more broadly across species. That is really a new revolution." Explore further: Team identifies molecular 'finger' that pushes the domino of life


Thestrup T.,Max Planck Institute of Neurobiology | Thestrup T.,Howard Hughes Medical Institute | Litzlbauer J.,Max Planck Institute of Neurobiology | Bartholomaus I.,Max Planck Institute of Neurobiology | And 19 more authors.
Nature Methods | Year: 2014

The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sensor. These 'Twitch' sensors are based on the C-terminal domain of Opsanus troponin C. Their FRET responses were optimized by a large-scale functional screen in bacterial colonies, refined by a secondary screen in rat hippocampal neuron cultures. We tested the in vivo performance of the most sensitive variants in the brain and lymph nodes of mice. The sensitivity of the Twitch sensors matched that of synthetic calcium dyes and allowed visualization of tonic action potential firing in neurons and high resolution functional tracking of T lymphocytes. Given their ratiometric readout, their brightness, large dynamic range and linear response properties, Twitch sensors represent versatile tools for neuroscience and immunology. © 2014 Nature America, Inc. All rights reserved.


Nelson F.E.,University of Pennsylvania | Nelson F.E.,Whitman Center | Nelson F.E.,Temple University | Hollingworth S.,University of Pennsylvania | And 3 more authors.
Journal of General Physiology | Year: 2014

The mating call of the Atlantic toadfish is generated by bursts of high-frequency twitches of the superfast twitch fibers that surround the swimbladder. At 16°C, a calling period can last several hours, with individual 80-100-Hz calls lasting ~500 ms interleaved with silent periods (intercall intervals) lasting ~10 s. To understand the intracellular movements of Ca2+ during the intercall intervals, superfast fibers were microinjected with fluo-4, a high-affinity fluorescent Ca2+ indicator, and stimulated by trains of 40 action potentials at 83 Hz, which mimics fiber activity during calling. The fluo-4 fluorescence signal was measured during and after the stimulus trains; the signal was also simulated with a kinetic model of the underlying myoplasmic Ca2+ movements, including the binding and transport of Ca2+ by the sarcoplasmic reticulum (SR) Ca2+ pumps. The estimated total amount of Ca2+ released from the SR during a first stimulus train is ~6.5 mM (concentration referred to the myoplasmic water volume). At 40 ms after cessation of stimulation, the myoplasmic free Ca2+ concentration ([Ca2+]) is below the threshold for force generation (~3 μM), yet the estimated concentration of released Ca2+ remaining in the myoplasm (~[CaM]) is large, ~5 mM, with ~80% bound to parvalbumin. At 10 s after stimulation, [Ca2+] is ~90 nM (three times the assumed resting level) and ~[CaM] is ~1.3 mM, with 97% bound to parvalbumin. Ca2+ movements during the intercall interval thus appear to be strongly influenced by (a) the accumulation of Ca2+ on parvalbumin and (b) the slow rate of Ca2+ pumping that ensues when parvalbumin lowers [Ca2+] near the resting level. With repetitive stimulus trains initiated at 10-s intervals, Ca2+ release and pumping come quickly into balance as a result of the stability (negative feedback) supplied by the increased rate of Ca2+ pumping at higher [Ca2+]. © 2014 Nelson et al.


Elemans C.P.H.,National Oceanic and Atmospheric Administration | Elemans C.P.H.,University of Southern Denmark | Mensinger A.F.,Whitman Center | Mensinger A.F.,University of Minnesota | And 2 more authors.
Journal of Experimental Biology | Year: 2014

Sound communication is fundamental to many social interactions and essential to courtship and agonistic behaviours in many vertebrates. The swimbladder and associated muscles in batrachoidid fishes (midshipman and toadfish) is a unique vertebrate sound production system, wherein fundamental frequencies are determined directly by the firing rate of a vocal-acoustic neural network that drives the contraction frequency of superfast swimbladder muscles. The oyster toadfish boatwhistle call starts with an irregular sound waveform that could be an emergent property of the peripheral nonlinear sound-producing system or reflect complex encoding in the central nervous system. Here, we demonstrate that the start of the boatwhistle is indicative of a chaotic strange attractor, and tested whether its origin lies in the peripheral sound-producing system or in the vocal motor network. We recorded sound and swimbladder muscle activity in awake, freely behaving toadfish during motor nerve stimulation, and recorded sound, motor nerve and muscle activity during spontaneous grunts. The results show that rhythmic motor volleys do not cause complex sound signals. However, arrhythmic recruitment of swimbladder muscle during spontaneous grunts correlates with complex sounds. This supports the hypothesis that the irregular start of the boatwhistle is encoded in the vocal pre-motor neural network, and not caused by peripheral interactions with the sound-producing system. We suggest that sound production system demands across vocal tetrapods have selected for muscles and motorneurons adapted for speed, which can execute complex neural instructions into equivalently complex vocalisations. © 2014, Company of Biologists Ltd. All rights reserved.


Lucas K.N.,Roger Williams University | Lucas K.N.,Harvard University | Johnson N.,Providence College | Johnson N.,Texas A&M University at Galveston | And 10 more authors.
Nature Communications | Year: 2014

Animal propulsors such as wings and fins bend during motion and these bending patterns are believed to contribute to the high efficiency of animal movements compared with those of man-made designs. However, efforts to implement flexible designs have been met with contradictory performance results. Consequently, there is no clear understanding of the role played by propulsor flexibility or, more fundamentally, how flexible propulsors should be designed for optimal performance. Here we demonstrate that during steady-state motion by a wide range of animals, from fruit flies to humpback whales, operating in either air or water, natural propulsors bend in similar ways within a highly predictable range of characteristic motions. By providing empirical design criteria derived from natural propulsors that have convergently arrived at a limited design space, these results provide a new framework from which to understand and design flexible propulsors. © 2014 Macmillan Publishers Limited. All rights reserved.


Santhanakrishnan A.,Georgia Institute of Technology | Dollinger M.,University of North Carolina at Chapel Hill | Hamlet C.L.,North Carolina State University | Colin S.P.,Roger Williams University | And 2 more authors.
Journal of Experimental Biology | Year: 2012

Quantifying the flows generated by the pulsations of jellyfish bells is crucial for understanding the mechanics and efficiency of their swimming and feeding. Recent experimental and theoretical work has focused on the dynamics of vortices in the wakes of swimming jellyfish with relatively simple oral arms and tentacles. The significance of bell pulsations for generating feeding currents through elaborate oral arms and the consequences for particle capture are not as well understood. To isolate the generation of feeding currents from swimming, the pulsing kinematics and fluid flow around the benthic jellyfish Cassiopea spp. were investigated using a combination of videography, digital particle image velocimetry and direct numerical simulation. During the rapid contraction phase of the bell, fluid is pulled into a starting vortex ring that translates through the oral arms with peak velocities that can be of the order of 10?cm?s-1. Strong shear flows are also generated across the top of the oral arms throughout the entire pulse cycle. A coherent train of vortex rings is not observed, unlike in the case of swimming oblate medusae such as Aurelia aurita. The phase-Averaged flow generated by bell pulsations is similar to a vertical jet, with induced flow velocities averaged over the cycle of the order of 1-10?mm?s-1. This introduces a strong near-horizontal entrainment of the fluid along the substrate and towards the oral arms. Continual flow along the substrate towards the jellyfish is reproduced by numerical simulations that model the oral arms as a porous Brinkman layer of finite thickness. This two-dimensional numerical model does not, however, capture the far-field flow above the medusa, suggesting that either the three-dimensionality or the complex structure of the oral arms helps to direct flow towards the central axis and up and away from the animal. © 2012. Published by The Company of Biologists Ltd.

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