Anderson C.T.,University of Pittsburgh |
Radford R.J.,Massachusetts Institute of Technology |
Zastrow M.L.,Massachusetts Institute of Technology |
Zhang D.Y.,Massachusetts Institute of Technology |
And 4 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015
Many excitatory synapses contain high levels of mobile zinc within glutamatergic vesicles. Although synaptic zinc and glutamate are coreleased, it is controversial whether zinc diffuses away from the release site or whether it remains bound to presynaptic membranes or proteins after its release. To study zinc transmission and quantify zinc levels, we required a high-affinity rapid zinc chelator as well as an extracellular ratiometric fluorescent zinc sensor. We demonstrate that tricine, considered a preferred chelator for studying the role of synaptic zinc, is unable to efficiently prevent zinc from binding low-nanomolar zinc-binding sites, such as the high-affinity zinc-binding site found in NMDA receptors (NMDARs). Here, we used ZX1, which has a 1 nM zinc dissociation constant and second-order rate constant for binding zinc that is 200-fold higher than those for tricine and CaEDTA. We find that synaptic zinc is phasically released during action potentials. In response to short trains of presynaptic stimulation, synaptic zinc diffuses beyond the synaptic cleft where it inhibits extrasynaptic NMDARs. During higher rates of presynaptic stimulation, released glutamate activates additional extrasynaptic NMDARs that are not reached by synaptically released zinc, but which are inhibited by ambient, tonic levels of nonsynaptic zinc. By performing a ratiometric evaluation of extracellular zinc levels in the dorsal cochlear nucleus, we determined the tonic zinc levels to be low nanomolar. These results demonstrate a physiological role for endogenous synaptic as well as tonic zinc in inhibiting extrasynaptic NMDARs and thereby fine tuning neuronal excitability and signaling. © 2015, National Academy of Sciences. All rights reserved.
Corrales-Ugalde M.,University of Oregon |
Colin S.P.,Roger Williams University |
Colin S.P.,Whitman Center |
Sutherland K.R.,University of Oregon
Marine Ecology Progress Series | Year: 2017
Understanding the factors that control predation in pelagic communities can inform predictions of community structure in marine ecosystems. Ubiquitous and selective predators such as cnidarian hydromedusae rely on their nematocysts to capture and retain prey but it is not clear how the density and spatial distribution of these cells relate to predation mode. We examined the relationship between prey capture and nematocyst distribution in the tentacles of Aglantha digitale and Proboscidactyla flavicirrata, which are considered ambush predators, and Clytia gregaria and Mitrocoma cellularia, which are considered feeding-current predators. First, we analyzed video of predator-prey interactions to compare capture locations of Artemia nauplii relative to the bell margin of each species. Second, tentacles of the same 4 species plus Sarsia tubulosa and Aequorea Victoria were analyzed using microscopy to determine nematocyst distribution along their lengths. By analyzing behavior and morphology simultaneously, we found that the ambush predators A. digitale and P. flavicirrata have higher nematocyst density far from the bell and tend to capture more prey in the same region. In contrast, the feeding-current predators C. gregaria and M. cellularia capture most of their prey close to the bell, where they also show a slight increase in nematocyst densities. The presence of high nematocyst densities in regions where prey are likely to contact feeding structures serves to increase capture efficiencies. Quantifying the relationship between prey capture and nematocyst locations for different foraging strategies will strengthen the ability of researchers to predict feeding behavior based on morphological features. © 2017 Inter-Research.
Joshi A.,University of Pittsburgh |
Middleton J.W.,University of Pittsburgh |
Anderson C.T.,University of Pittsburgh |
Borges K.,Northwestern University |
And 4 more authors.
Journal of Neuroscience | Year: 2015
Auditory cortex (AC) layer 5B (L5B) contains both corticocollicular neurons, a type of pyramidal-tract neuron projecting to the inferior colliculus, and corticocallosal neurons, a type of intratelencephalic neuron projecting to contralateral AC. Although it is known that these neuronal types have distinct roles in auditory processing and different response properties to sound, the synaptic and intrinsic mecha-nisms shaping their input-output functions remain less understood. Here, we recorded in brain slices of mouse AC from retrogradely labeled corticocollicular and neighboring corticocallosal neurons in L5B. Corticocollicular neurons had, on average, lower input resis-tance, greater hyperpolarization-activated current (Ih), depolarized resting membrane potential, faster action potentials, initial spike doublets, and less spike-frequency adaptation. In paired recordings between single L2/3 and labeled L5B neurons, the probabilities of connection, amplitude, latency, rise time, and decay time constant of the unitary EPSC were not different for L2/3→corticocollicular and L2/3→corticocallosal connections. However, short trains of unitary EPSCs showed no synaptic depression in L2/3→corticocollicular connections, but substantial depression in L2/3→corticocallosal connections. Synaptic potentials in L2/3→corticocollicular connec-tions decayed faster and showed less temporal summation, consistent with increased Ih in corticocollicular neurons, whereas synaptic potentials in L2/3→corticocallosal connections showed more temporal summation. Extracellular L2/3 stimulation at two different rates resulted in spiking in L5B neurons; for corticocallosal neurons the spike rate was frequency dependent, but for corticocollicular neurons it was not. Together, these findings identify cell-specific intrinsic and synaptic mechanisms that divide intracortical synaptic excitation from L2/3 to L5B into two functionally distinct pathways with different input-output functions. © 2015 the authors.
Gemmell B.J.,University of Texas at Austin |
Gemmell B.J.,Whitman Center |
Sheng J.,University of Minnesota |
Sheng J.,Texas Tech University |
Buskey E.J.,University of Texas at Austin
Proceedings of the National Academy of Sciences of the United States of America | Year: 2013
Despite high predation pressure, planktonic copepods remain one of the most abundant groups on the planet. Their escape response provides one of most effective mechanisms to maximize evolutionary fitness. Owing to their small size (100 μm) compared with their predators (>1 mm), increasing viscosity is believed to have detrimental effects on copepods' fitness at lower temperature. Using high-speed digital holography we acquire 3D kinematics of the nauplius escape including both location and detailed appendage motion. By independently varying temperature and viscosity we demonstrate that at natural thermal extremes, contrary to conventional views, nauplii achieve equivalent escape distance while maintaining optimal velocity. Using experimental results and kinematic simulations from a resistive force theory propulsion model, we demonstrate that a shift in appendage timing creates an increase in power stroke duration relative to recovery stroke duration. This change allows the nauplius to limit losses in velocity and maintain distance during escapes at the lower bound of its natural thermal range. The shift in power stroke duration relative to recovery stroke duration is found to be regulated by the temperature dependence of swimming appendage muscle groups, not a dynamic response to viscosity change. These results show that copepod nauplii have natural adaptive mechanisms to compensate for viscosity variations with temperature but not in situations in which viscosity varies independent of temperature, such as in some phytoplankton blooms. Understanding the robustness of escapes in the wake of environmental changes such as temperature and viscosity has implications in assessing the future health of performance compensation.
News Article | April 20, 2016
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
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 | December 27, 2016
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
News Article | April 28, 2016
"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
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.
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.