The Possible Role of Molecular Vibration in Intracellular Signalling
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Wnt Signaling in Vertebrate Neural Development and Function
J Neuroimmune Pharmacol (2012) 7:774–787 DOI 10.1007/s11481-012-9404-x INVITED REVIEW Wnt Signaling in Vertebrate Neural Development and Function Kimberly A. Mulligan & Benjamin N. R. Cheyette Received: 18 June 2012 /Accepted: 10 September 2012 /Published online: 27 September 2012 # Springer Science+Business Media, LLC 2012 Abstract Members of the Wnt family of secreted signaling immature neurons migrate to populate different cortical proteins influence many aspects of neural development and layers, nuclei, and ganglia in the forebrain, midbrain, hind- function. Wnts are required from neural induction and axis brain, and spinal cord. Each mature neuron elaborates an formation to axon guidance and synapse development, and axon and numerous dendrites while forming hundreds to even help modulate synapse activity. Wnt proteins activate a thousands of synapses with other neurons, enabling electro- variety of downstream signaling pathways and can induce a chemical communication throughout the nervous system. similar variety of cellular responses, including gene tran- All these developmental processes must be coordinated to scription changes and cytoskeletal rearrangements. This re- ensure proper construction and function of the CNS, and view provides an introduction to Wnt signaling pathways this requires the coordinated developmental activity of a and discusses current research on their roles in vertebrate vast array of genes. neural development and function. Members of the Wnt family of secreted signaling proteins are implicated in every step of neural development men- Keywords Wnt signaling . Neural development . tioned above. Wnt proteins provide positional information CNS patterning . Axon guidance . Dendrite growth . within the embryo for anterior-posterior axis specification of Synapse formation . -
DIXDC1 Contributes to Psychiatric Susceptibility by Regulating Dendritic Spine and Glutamatergic Synapse Density Via GSK3 and Wnt/Β-Catenin Signaling
DIXDC1 contributes to psychiatric susceptibility by regulating dendritic spine and glutamatergic synapse density via GSK3 and Wnt/β-catenin signaling The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Martin, P., R. E. Stanley, A. P. Ross, A. E. Freitas, C. E. Moyer, A. C. Brumback, J. Iafrati, et al. 2016. “DIXDC1 contributes to psychiatric susceptibility by regulating dendritic spine and glutamatergic synapse density via GSK3 and Wnt/β-catenin signaling.” Molecular psychiatry :10.1038/mp.2016.184. doi:10.1038/mp.2016.184. http:// dx.doi.org/10.1038/mp.2016.184. Published Version doi:10.1038/mp.2016.184 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:32630523 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Mol Psychiatry Manuscript Author . Author Manuscript Author manuscript; available in PMC 2017 April 19. DIXDC1 contributes to psychiatric susceptibility by regulating dendritic spine and glutamatergic synapse density via GSK3 and Wnt/β-catenin signaling Pierre-Marie Martin#1, Robert E. Stanley#1,2, Adam P. Ross#1, Andiara E. Freitas#1, Caitlin E. Moyer3, Audrey C. Brumback1,4, Jillian Iafrati1, Kristina S. Stapornwongkul1, Sky Dominguez1, Saul Kivimäe1, Kimberly A. Mulligan1,5, Mehdi Pirooznia6, W. Richard McCombie7, James B. Potash8, Peter P. Zandi9, Shaun M. -
PIP3-Phldb2 Is Crucial for LTP Regulating Synaptic NMDA and AMPA Receptor Density and PSD95 Turnover
国立大学法人電気通信大学 / The University of Electro-Communications PIP3-Phldb2 is crucial for LTP regulating synaptic NMDA and AMPA receptor density and PSD95 turnover 著者(英) Min-Jue Xie, Yasuyuki Ishikawa, Hideshi Yagi, Tokuichi Iguchi, Yuichiro Oka, Kazuki Kuroda, Keiko Iwata, Hiroshi Kiyonari, Shinji Matsuda, Hideo Matsuzaki, Michisuke Yuzaki, Yugo Fukazawa, Makoto Sato journal or Scientific Reports publication title volume 9 number 1 page range 4305 year 2019-03-13 URL http://id.nii.ac.jp/1438/00009269/ doi: 10.1038/s41598-019-40838-6 Creative Commons Attribution 4.0 International License www.nature.com/scientificreports OPEN PIP3-Phldb2 is crucial for LTP regulating synaptic NMDA and AMPA receptor density and PSD95 Received: 1 November 2018 Accepted: 11 February 2019 turnover Published: xx xx xxxx Min-Jue Xie1,2,3,4,5, Yasuyuki Ishikawa6,7, Hideshi Yagi1,8, Tokuichi Iguchi1,9, Yuichiro Oka1,5,9, Kazuki Kuroda1,2,4, Keiko Iwata3,4,5, Hiroshi Kiyonari10, Shinji Matsuda11,12,13, Hideo Matsuzaki3,5, Michisuke Yuzaki 11, Yugo Fukazawa 2,3,4 & Makoto Sato 1,3,5,9 The essential involvement of phosphoinositides in synaptic plasticity is well-established, but incomplete knowledge of the downstream molecular entities prevents us from understanding their signalling cascades completely. Here, we determined that Phldb2, of which pleckstrin-homology domain is highly sensitive to PIP3, functions as a phosphoinositide-signalling mediator for synaptic plasticity. BDNF application caused Phldb2 recruitment toward postsynaptic membrane in dendritic spines, whereas PI3K inhibition resulted in its reduced accumulation. Phldb2 bound to postsynaptic scafolding molecule PSD-95 and was crucial for localization and turnover of PSD-95 in the spine. -
The Molecular Design of Visual Transduction
The Molecular Design of Visual Transduction Tomoki Isayama1, Anita L. Zimmerman2, Clint L. Makino1 1Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA 02114; 2Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912 Our daily lives are so resplendent with activities that include or require vision, that it is easy to overlook the complexity of the underlying processes involved. Here we describe the first step in vision…detection of light by our photoreceptors. This input stage sets limits on what we can and cannot see. The goal of this resource page is to impart a better understanding of the molecular design behind visual transduction. Structure and Function of Rods and Cones The photoreceptors are located in the deepest layer of the retina (Fig.1), farthest from the incoming light. There are two kinds, rods and cones, so named for their overall shapes. Rods operate in very low light, such as at night. Cones operate under brighter conditions and provide the basic units for color vision. The recently discovered intrinsically photoreceptive ganglion cells will be excluded from this review because while they respond to light, they have not been shown to contribute to image-forming vision. Rods and cones are specialized unipolar neurons. All vertebrate visual receptors follow a simple blueprint. They can be divided into two portions, termed inner and outer segments, according to their radial position within the retina (Fig.1B). The inner segment consists of the cell body and contains the cellular organelles found in other neurons, including a synaptic terminal. -
TBX3 Acts As Tissue-Specific Component of the Wnt/Β
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.22.053561; this version posted April 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. TBX3 acts as tissue-specific component of the Wnt/b-catenin enhanceosome Dario Zimmerli1,6#, Costanza Borrelli2#, Amaia Jauregi-Miguel3,4#, Simon Söderholm3,4, Salome Brütsch1, Nikolaos Doumpas1, Jan Reichmuth1, Fabienne Murphy-Seiler5, Michel Aguet5, Konrad Basler1*, Andreas E. Moor2*, Claudio Cantù3,4* 1 Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland, CH-8057 2 Institute of Molecular Cancer Research, University of Zurich, Zürich, Switzerland, CH-8057 3 Wallenberg Centre for Molecular Medicine, Linköping University 4 Department of Biomedical and Clinical Sciences, Faculty of Health Science, SE-581 83 Linköping, Sweden 5Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, CH-1015 Lausanne, Switzerland 6 Current address: Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands # These authors contributed equally to this work * For correspondence: [email protected] [email protected] [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.22.053561; this version posted April 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. -
Technical Application Note
Compact Rugged Spectrometers - A Universe of Spectroscopy Systems Technical Application Note Vibrational Spectroscopy: Infrared vs. Raman StellarNet, Inc. Tampa, Fl USA Tony Rizzuto, PhD April 12, 2017 Vibrational spectroscopies are integral in analyzing some of the most fundamentally important processes in physical chemistry: molecular vibrations. While there are many different experimental techniques used to analyze those vibrations, most are variations of the “Big Two,” FTIR and Raman scattering spectroscopies. This article aims to analyze the benefits and drawbacks of each of the “Big Two,” with the hope that it helps one choose the correct technique for one’s research interests. 1. What are the “Big Two?” Fourier Transform Infrared Spectroscopy Raman spectroscopy relies on inelastic (FTIR) is a simple absorption measurement scattering phenomenon that probes the where the detector measures the molecular vibration. Where FTIR will use a absorbance of infrared radiation by the broadband IR source, Raman spectroscopy sample. Each sample will absorb different typically uses a narrow-band, amounts of each frequency resulting in a monochromatic light source in order to “chemical fingerprint” that is the FTIR excite the vibrations of the molecule in your spectrum. sample. 2. Selection Rules: What molecular vibrations are being probed? Imagining a molecular bond vibration with the traditional ball and spring model (Figure 1a) and its resultant harmonic oscillator depiction (Figure 1b) allows us to calculate the selection rules for vibrational transitions to be = 1. However, that does not tell the whole story. In order to truly differentiate FTIR from Raman Spectroscopy, we must think about it on a molecular level. Compact Rugged Spectrometers - A Universe of Spectroscopy Systems Technical Application Note A B Figure 1: A. -
Dominant Role of Tyrosine 394 Phosphorylation in Kinase Activity
MOLECULAR AND CELLULAR BIOLOGY, Sept. 1996, p. 4996–5003 Vol. 16, No. 9 0270-7306/96/$04.0010 Copyright q 1996, American Society for Microbiology Mutational Analysis of Lck in CD45-Negative T Cells: Dominant Role of Tyrosine 394 Phosphorylation in Kinase Activity 1 2 2 1 UGO D’ORO, KAZUYASU SAKAGUCHI, ETTORE APPELLA, AND JONATHAN D. ASHWELL * Laboratory of Immune Cell Biology1 and Laboratory of Cell Biology,2 National Cancer Institute, Bethesda, Maryland 20892 Received 29 November 1995/Returned for modification 30 January 1996/Accepted 18 June 1996 The CD45 tyrosine phosphatase has been reported to activate the src family tyrosine kinases Lck and Fyn by dephosphorylating regulatory COOH-terminal tyrosine residues 505 and 528, respectively. However, recent studies with CD452 T-cell lines have found that despite the fact that Lck and Fyn were constitutively hyperphosphorylated, the tyrosine kinase activity of both enzymes was actually increased. In the present study, phosphoamino acid analysis revealed that the increased phosphorylation of Lck in CD452 YAC-1 T cells was restricted to tyrosine residues. To understand the relationship between tyrosine phosphorylation and Lck kinase activity, CD452 YAC-1 cells were transfected with forms of Lck in which tyrosines whose phosphory- lation is thought to regulate enzyme activity (Tyr-192, Tyr-394, Tyr-505, or both Tyr-394 and Tyr-505) were replaced with phenylalanine. While the Y-to-F mutation at position 192 (192-Y3F) had little effect, the 505-Y3F mutation increased enzymatic activity. In contrast, the 394-Y3F mutation decreased the kinase activity to very low levels, an effect that the double mutation, 394-Y3F and 505Y3F, could not reverse. -
1 Signal Duration and the Time Scale Dependence of Signal Integration in Biochemical Pathways Jason W. Locasale Department of Bi
1 Signal duration and the time scale dependence of signal integration in biochemical pathways Jason W. Locasale1 1Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139. [email protected] 2 Abstract Signal duration (e.g. the time scales over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments. Accompanying differences in signal duration are numerous downstream biological processes that require multiple steps of biochemical regulation. Here, we present an analysis that investigates how simple biochemical motifs that involve multiple stages of regulation can be constructed to differentially process signals that persist at different time scales. We compute the dynamic gain within these networks and resulting power spectra to better understand how biochemical networks can integrate signals at different time scales. We identify topological features of these networks that allow for different frequency dependent signal processing properties. Our studies suggest design principles for why signal duration in connection with multiple steps of downstream regulation is a ubiquitous control motif in biochemical systems. 3 Signal duration (e.g. the length of time over which a signaling intermediate is active) is a critical determinant in mediating cell decisions in numerous biological processes(Fig. 1) including cell growth, proliferation, and developmental lineage commitments (Marshall 1995; Chen et al. 1996; Dolmetsch et al. 1997; Chen et al. 2001; Murphy et al. 2002; Sasagawa et al. 2005; Murphy and Blenis 2006; Santos et al. 2007). One fundamental issue in signal transduction and cell decision making then is how differences in signal duration are detected to achieve the appropriate biological response. -
Neutron Vibrational Spectroscopy
Neutron Vibrational Spectroscopy A.J. (Timmy) Ramirez-Cuesta Luke L. Daemen Yongqiang Cheng Spallation Neutron Source Oak Ridge National Laboratory ORNL is managed by UT-Battelle for the US Department of Energy The S(Q,w) Map w=0 Elastic Scattering Diffraction Structural Information 2 "Let there be light" 3 4 How to measure INS (1) Direct Geometry Instrumentation 4000 3500 Direct geometry instruments 3000 ) 1 - m measure Q trajectory is c ( 2500 r e f determined by the angle s n 2000 a r t and energy transfer. y g r 1500 e n Examples: ARCS, CNCS, E HYSPEC, SEQUIOA 1000 500 0 0 10 20 30 Momentum transfer (A-1) ) . U . A ( y t i s n e L t 2 n I Incident neutron beam is 0 10 20 30 40 50 60 70 Energy (meV) s monochromatic t n u o c determining the incident n o r t u Distance energy E1. e N That determines T1. We L1 12000 13000 14000 15000 16000 measure the ToF and we ToF (ms) can work out T2. Resolution is almost constant in units of Ei time 5 VISION: a high throughput spectrometer for neutron vibrational spectroscopy Yongqiang Cheng, Luke Daemen, A.J. (Timmy) Ramirez-Cuesta Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, TN 37931 USA VISION offers users a variety of sample environments How to measure INS (2) Polybenzene nanothreads synthesized at high pressure: single nanothreads VISION is best thought of as and experimental/computational capabilities: the neutron analogue of a Structural inference through modeling of vibrational spectra Indirect Geometry Instrumentation Raman spectrometer. -
Femtosecond Time-Resolved Observation of Butterfly Vibration In
www.nature.com/scientificreports OPEN Femtosecond time-resolved observation of butterfy vibration in electronically excited Received: 7 June 2017 Accepted: 11 October 2017 o-fuorophenol Published: xx xx xxxx Fengzi Ling1,2, Shuai Li1,2, Xinli Song1,2, Yanmei Wang1,2, Jinyou Long1,2 & Bing Zhang 1,2 The butterfy vibration during the hydrogen tunneling process in electronically excited o-fuorophenol has been visualized in real time by femtosecond time-resolved ion yield spectroscopy coupled with time-resolved photoelectron imaging technique. A coherent superposition of out-of-plane C–F butterfy motions is prepared in the frst excited electronic state (S1). As the C–F bond vibrates with respect to the aromatic ring, the nuclear geometry varies periodically, leading to the corresponding variation in the photoionization channel. By virtue of the more favorable ionization probability from the nonplanar minimum via resonance with the Rydberg states, the evolution of the vibrational wave packet is manifested as a superimposed beat in the parent-ion transient. Moreover, time-resolved photoelectron spectra ofer a direct mapping of the oscillating butterfy vibration between the planar geometry and nonplanar minimum. The beats for the photoelectron peaks originating from the planar geometry are out of phase with those from the nonplanar minimum. Our results provide a physically intuitive and complete picture of the oscillatory fow of energy responsible for the coherent vibrational motion on the excited state surface. Ultrafast molecular vibration is one of the fundamental motions that characterize chemical bonding and decide reaction dynamics at the molecular level1–3. Over the past few decades, frequency-resolved spectroscopies such as infrared and Raman spectra4 and resonant two-photon ionization (R2PI) spectroscopy5 have devoted to pro- viding detailed spectroscopic data about molecular vibration. -
Cell Signaling As a Probabilistic Computer David Colliaux, Pierre Bessière, Jacques Droulez
Cell signaling as a probabilistic computer David Colliaux, Pierre Bessière, Jacques Droulez To cite this version: David Colliaux, Pierre Bessière, Jacques Droulez. Cell signaling as a probabilistic computer. Interna- tional Journal of Approximate Reasoning, Elsevier, 2016, 10.1016/j.ijar.2016.10.012. hal-01441464 HAL Id: hal-01441464 https://hal.archives-ouvertes.fr/hal-01441464 Submitted on 19 Jan 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Cell signaling as a probabilistic computer David Colliauxa, Pierre Bessièrea, Jacques Drouleza a CNRS - Sorbonne Universités/UPMC/ISIR Pyramide - T55/65 CC 173 - 4 Place Jussieu 75005 Paris France Abstract Living organisms survive and multiply even though they have uncertain and incomplete information about their envi- ronment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this challenge. Indeed, Bayesian inference is a way to do optimal reasoning when only uncertain and incomplete information is available. Various perceptive, sensory-motor, and cognitive functions have been successfully modeled this way. However, the biological mechanisms allowing animals and humans to represent and to compute probability distributions are not known. It has been proposed that neurons and assemblies of neurons could be the appropriate scale to search for clues to probabilistic reasoning. -
All-Digital Histopathology by Infrared-Optical Hybrid Microscopy
All-digital histopathology by infrared-optical hybrid microscopy Martin Schnella, Shachi Mittala,b, Kianoush Falahkheirkhaha,c, Anirudh Mittala,b, Kevin Yeha,b, Seth Kenkela,d, Andre Kajdacsy-Ballae, P. Scott Carneyf, and Rohit Bhargavaa,b,c,d,g,h,i,1 aBeckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL 61801; bDepartment of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801; cDepartment of Chemical and Biomolecular Engineering, University of Illinois at Urbana– Champaign, Urbana, IL 61801; dDepartment of Mechanical Science and Engineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801; eDepartment of Pathology, University of Illinois at Chicago, Chicago, IL 60612; fThe Institute of Optics, University of Rochester, Rochester, NY 14620; gCancer Center at Illinois, University of Illinois at Urbana–Champaign, Urbana, IL 61801; hDepartment of Electrical and Computer Engineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801; and iDepartment of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801 Edited by Christian Huck, University of Innsbruck, Innsbruck, Austria, and accepted by Editorial Board Member John A. Rogers December 20, 2019 (received for review July 19, 2019) Optical microscopy for biomedical samples requires expertise in fidelity imaging in both point-scanning (15) and wide-field (16–19) staining to visualize structure and composition. Midinfrared (mid-IR) modalities, IR pixel sizes are ∼100-fold larger than those easily spectroscopic imaging offers label-free molecular recording and achieved in visible microscopy, and data acquisition speed is still virtual staining by probing fundamental vibrational modes of three to four orders of magnitude slower than in visible imaging molecular components.