Pannexin 1 Transgenic Mice: Human Diseases and Sleep-Wake Function Revision
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Criticalreading #Wickedproblem
#CRITICALREADING #WICKEDPROBLEM We have a “wicked problem” . and that is a fantastic, engaging, exciting place to start. Carolyn V. Williams1 I. INTRODUCTION I became interested in the idea of critical reading—“learning to evaluate, draw inferences, and arrive at conclusions based on evidence” in the text2—when I assumed that my students would show up to law school with this skill . and then, through little fault of their own, they did not. I have not been the only legal scholar noticing this fact. During the 1980s and 90s a few legal scholars conducted research and wrote about law students’ reading skills.3 During the 2000s, a few more scholars wrote about how professors can help develop critical reading skills in law students.4 But it has not been until the past few years or so that legal scholars have begun to shine a light on just how deep the problem of law students’ critical reading skills 1 Professor Williams is an Associate Professor of Legal Writing & Assistant Clinical Professor of Law at the University of Arizona, James E. Rogers College of Law. Thank you to Dean Marc Miller for supporting this Article with a summer research grant. Many thanks to the Legal Writing Institute for hosting the 2018 We Write Retreat and the 2018 Writers’ Workshop and to the participants at each for their comments and support of this project. A heartfelt thank you to Mary Beth Beazley, Kenneth Dean Chestek, and Melissa Henke for graciously providing comments on prior drafts of this Article. Thank you to my oldest Generation Z child for demonstrating independence and the desire to fix broken systems so that I know my solution is possible. -
Mechanistic and Structural Studies of Pannexin Channels
MECHANISTIC AND STRUCTURAL STUDIES OF PANNEXIN CHANNELS A Dissertation Presented to the Faculty of the Graduate School of Cornell University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Kevin Ronald Michalski August 2018 © 2018 Kevin Ronald Michalski MECHANISTIC AND STRUCTURAL STUDIES OF PANNEXIN CHANNELS Kevin Ronald Michalski, Ph.D Cornell University 2018 Pannexin channels are a family of recently discovered membrane proteins found in nearly every tissue of the human body. These channels have been classified as large ‘pore forming’ proteins which, when activated, create a passageway through the cell membrane through which ions and molecules transit. Current literature suggests that the actual pannexin channel is formed from a hexameric arrangement of individual monomeric pannexin subunits, resulting in a central permeation pathway for conducting ions. Opening of pannexin channels can be accomplished through several mechanisms. During apoptosis, for example, cleavage of the pannexin C-terminal domain results in a constitutively open channel through which ATP is released. However, curiously, pannexins have also been known to be activated by a variety of other stimuli such as cellular depolarization, exposure to signaling ions like Ca2+ and K+, and interacting with various other membrane receptors like members of the ATP- sensing P2X and P2Y family. How can pannexin channels sense and respond to such a diverse array of stimuli, and what is the fundamental ‘gating process’ that defines channel opening? Here, we use electrophysiology to study the activation of pannexin-1 (Panx1). We used a protein chimera approach to identify that the first extracellular domain of Panx1 is critical for inhibitor action. -
GPCR Regulation of ATP Efflux from Astrocytes
G PROTEIN-COUPLED RECEPTOR REGULATION OF ATP RELEASE FROM ASTROCYTES by ANDREW EDWARD BLUM Thesis advisor: Dr. George R. Dubyak Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Department of Physiology and Biophysics CASE WESTERN RESERVE UNIVERSITY May, 2010 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of _____________________________________________________ candidate for the ______________________degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. Dedication I am greatly indebted to my thesis advisor Dr. George Dubyak. Without his support, patience, and advice this work would not have been possible. I would also like to acknowledge Dr. Robert Schleimer and Dr. Walter Hubbard for their encouragement as I began my research career. My current and past thesis committee members Dr. Matthias Buck, Dr. Cathleen Carlin, Dr. Edward Greenfield, Dr. Ulrich Hopfer, Dr. Gary Landreth, Dr. Corey Smith, Dr. Jerry Silver have provided invaluable guidance and advice for which I am very grateful. A special thanks to all of the past and present -
Generation Times of E. Coli Prolong with Increasing Tannin Concentration While the Lag Phase Extends Exponentially
plants Article Generation Times of E. coli Prolong with Increasing Tannin Concentration while the Lag Phase Extends Exponentially Sara Štumpf 1 , Gregor Hostnik 1, Mateja Primožiˇc 1, Maja Leitgeb 1,2 and Urban Bren 1,3,* 1 Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor 2000, Slovenia; [email protected] (S.Š.); [email protected] (G.H.); [email protected] (M.P.); [email protected] (M.L.) 2 Faculty of Medicine, University of Maribor, Maribor 2000, Slovenia 3 Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper 6000, Slovenia * Correspondence: [email protected]; Tel.: +386-2-2294-421 Received: 18 November 2020; Accepted: 29 November 2020; Published: 1 December 2020 Abstract: The current study examines the effect of tannins and tannin extracts on the lag phase duration, growth rate, and generation time of Escherichia coli.Effects of castalagin, vescalagin, gallic acid, Colistizer, tannic acid as well as chestnut, mimosa, and quebracho extracts were determined on E. coli’s growth phases using the broth microdilution method and obtained by turbidimetric measurements. E. coli responds to the stress caused by the investigated antimicrobial agents with reduced growth rates, longer generation times, and extended lag phases. Prolongation of the lag phase was relatively small at low tannin concentrations, while it became more pronounced at concentrations above half the MIC. Moreover, for the first time, it was observed that lag time extensions follow a strict exponential relationship with increasing tannin concentrations. This feature is very likely a direct consequence of the tannin complexation of certain essential ions from the growth medium, making them unavailable to E. -
The Following Paper Posted Here Is Not the Official IEEE Published Version
The following paper posted here is not the official IEEE published version. The final published version of this paper can be found in the Proceedings of the IEEE International Conference on Communication, Volume 3:pp.1490-1494 Copyright © 2004 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. Investigation and modeling of traffic issues in immersive audio environments Jeremy McMahon, Michael Rumsewicz Paul Boustead, Farzad Safaei TRC Mathematical Modelling Telecommunications and Information Technology Research University of Adelaide Institute South Australia 5005, AUSTRALIA University of Wollongong jmcmahon, [email protected] New South Wales 2522, AUSTRALIA [email protected], [email protected] Abstract—A growing area of technical importance is that of packets being queued at routers. distributed virtual environments for work and play. For the This is an area that has not undergone significant research audio component of such environments to be useful, great in the literature. Most of the available literature regarding emphasis must be placed on the delivery of high quality audio synchronization in multimedia relates to synchronizing audio scenes in which participants may change their relative positions. with video playout (e.g. [5], [6], [7]) and / or requires a global In this paper we describe and analyze an algorithm focused on maintaining relative synchronization between multiple users of synchronization clock such as GPS (e.g. -
Therapeutic Nanobodies Targeting Cell Plasma Membrane Transport Proteins: a High-Risk/High-Gain Endeavor
biomolecules Review Therapeutic Nanobodies Targeting Cell Plasma Membrane Transport Proteins: A High-Risk/High-Gain Endeavor Raf Van Campenhout 1 , Serge Muyldermans 2 , Mathieu Vinken 1,†, Nick Devoogdt 3,† and Timo W.M. De Groof 3,*,† 1 Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; [email protected] (R.V.C.); [email protected] (M.V.) 2 Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; [email protected] 3 In Vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; [email protected] * Correspondence: [email protected]; Tel.: +32-2-6291980 † These authors share equal seniorship. Abstract: Cell plasma membrane proteins are considered as gatekeepers of the cell and play a major role in regulating various processes. Transport proteins constitute a subclass of cell plasma membrane proteins enabling the exchange of molecules and ions between the extracellular environment and the cytosol. A plethora of human pathologies are associated with the altered expression or dysfunction of cell plasma membrane transport proteins, making them interesting therapeutic drug targets. However, the search for therapeutics is challenging, since many drug candidates targeting cell plasma membrane proteins fail in (pre)clinical testing due to inadequate selectivity, specificity, potency or stability. These latter characteristics are met by nanobodies, which potentially renders them eligible therapeutics targeting cell plasma membrane proteins. Therefore, a therapeutic nanobody-based strategy seems a valid approach to target and modulate the activity of cell plasma membrane Citation: Van Campenhout, R.; transport proteins. -
Ubiquitination and Proteasomal Regulation of Pannexin 1 and Pannexin 3
Ubiquitination and proteasomal regulation of Pannexin 1 and Pannexin 3 Anna Blinder A thesis submitted in partial fulfillment of the requirements for the Master’s degree in Cellular and Molecular Medicine Department of Cellular and Molecular Medicine Faculty of Medicine University of Ottawa © Anna Blinder, Ottawa, Canada, 2020 ABSTRACT Pannexin 1 (PANX1) and Pannexin 3 (PANX3) are single-membrane channel glycoproteins that allow for communication between the cell and its environment to regulate cellular differentiation, proliferation, and apoptosis. Their expression is regulated through post-translational modifications, however, their regulation by ubiquitination and the ubiquitin proteasome pathway (UPP) has not been examined. Here, I show that PANX1 is monoubiquitinated and K48- and K63-polyubiquitinated, and PANX3 is polyubiquitinated. While treatment with MG132 altered the banding profile and subcellular distribution of both pannexins, data suggested that only PANX3 is degraded by the UPP. To study the purpose of PANX1 ubiquitination, a PANX1 mutant bearing nine lysine mutations was engineered. Results revealed increased cell surface expression of the mutant, suggesting that ubiquitination may regulate trafficking. I thus demonstrated for the first time that PANX1 and PANX3 are polyubiquitinated and differentially regulated by ubiquitin and by the proteasome, indicating distinct mechanisms that stringently regulate pannexin expression. II TABLE OF CONTENTS ABSTRACT ............................................................................................................................................... -
Cryo-EM Structure of the Volume-Regulated Anion Channel
bioRxiv preprint doi: https://doi.org/10.1101/331207; this version posted May 25, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Cryo-EM structure of the volume-regulated anion channel LRRC8 Go Kasuya1*, Takanori Nakane1†*, Takeshi Yokoyama2*, Yanyan Jia3, Masato Inoue4, Kengo Watanabe4, Ryoki Nakamura1, Tomohiro Nishizawa1, Tsukasa Kusakizako1, Akihisa Tsutsumi5, Haruaki Yanagisawa5, Naoshi Dohmae6, Motoyuki Hattori7, Hidenori Ichijo4, Zhiqiang Yan3, Masahide Kikkawa5, Mikako Shirouzu2, Ryuichiro Ishitani1, Osamu Nureki1‡ 1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; 2Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan; 3State Key Laboratory of Medical Neurobiology, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China; 4Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; 5Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; 6RIKEN, Global Research Cluster, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; 7State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China. -
Chapter 04 Lecture
Chapter 04 Lecture 1 A GLIMPSE OF HISTORY German physician Robert Koch (1843–1910) Studied disease-causing bacteria; Nobel Prize in 1905 Developed methods of cultivating bacteria Worked on methods of solid media to allow single bacteria to grow and form colonies Tried potatoes, but nutrients limiting for many bacteria • Solidifying liquid nutrient media with gelatin helped • Limitations: melting temperature, digestible • In 1882, Fannie Hess, wife of associate, suggested agar, then used to harden jelly INTRODUCTION Prokaryotes found growing in severe conditions Ocean depths, volcanic vents, polar regions all harbor thriving prokaryotic species Many scientists believe that if life exists on other planets, it may resemble these microbes Individual species have limited set of conditions Also require appropriate nutrients Important to grow microbes in culture Medical significance Nutritional, industrial uses 4.1. PRINCIPLES OF BACTERIAL GROWTH Prokaryotic cells divide by binary fission Cell gets longer and One cell divides into two, two DNA replicates. into four, 48, 816, etc… Exponential growth: population DNA is moved into each future daughter doubles each division cell and cross wall forms. Generation time is time it takes to double Varies among species Cell divides into two cells. Environmental conditions Exponential growth has important consequences Cells separate. 10 cells of food-borne pathogen in potato salad at picnic can become 40,000 cells in 4 hours Daughter cells 4.1. PRINCIPLES OF BACTERIAL GROWTH Growth can be calculated n Nt = N0 x 2 Nt = number of cells in population at time t N0 = original number of cells in population n = number of divisions Example: pathogen in potato salad at picnic in sun Assume 10 cells with 20 minute generation time N0 = 10 cells in original population n = 12 (3 divisions per hour for 4 hours) n 12 Nt = N0 x 2 = 10 x 2 Nt = 10 x 4,096 Nt = 40,960 cells of pathogen in 4 hours! 4.1. -
A Theory for the Age and Generation Time Distribution of a Microbial Population
Journal of Mathematical Biology 1, 17--36 (1974) by Springer-Verlag 1974 A Theory for the Age and Generation Time Distribution of a Microbial Population J. L. Lebowitz* and S. I. Rubinow, New York Received October 9, 1973 Summary A theory is presented for the time evolution of the joint age and generation time distribution of a microbial population. By means of the solution to the fundamental equation of the theory, the effect of correlations between the generation times of mother and daughter cells may be determined on the transient and steady state growth stages of the population. The relationships among various generation time distributions measured under different experimental circumstances is clarified. 1. Introduction A striking property of microbial populations, even when grown under constant environmental conditions, is the great variability of the generation times of individual members of the population, illustrated in Fig. 1. The cause of this variability remains an important unsolved biological problem. The variability is generally ascribed to intrinsic variable factors associated with cell growth and maturation, culminating in division [1]. Prescott [2] has suggested that the variability stems from variability in the initial state of a newborn cell, where initial state means cell weight, number of mitochondria, microsomes, etc. Variability in the initial state of the chromosome is likewise a fundamental feature of the Cooper-Helmstetter model for chromo- some replication in E. coli [3]. In both of these views, the generation time is determined at birth. * Also Physics Department, Belfer Graduate School of Sciences, Yeshiva University, New York, NY 10019, U.S.A. Journ. -
Causemap: Fast Inference of Causality from Complex Time Series
CauseMap: fast inference of causality from complex time series M. Cyrus Maher1 and Ryan D. Hernandez2,3,4 1 Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA 2 Department of Bioengineering and Therapeutic Sciences, USA 3 Institute for Human Genetics, USA 4 Institute for Quantitative Biosciences (QB3), University of California, San Francisco, CA, USA ABSTRACT Background. Establishing health-related causal relationships is a central pursuit in biomedical research. Yet, the interdependent non-linearity of biological systems renders causal dynamics laborious and at times impractical to disentangle. This pursuit is further impeded by the dearth of time series that are suYciently long to observe and understand recurrent patterns of flux. However, as data generation costs plummet and technologies like wearable devices democratize data collection, we anticipate a coming surge in the availability of biomedically-relevant time series data. Given the life-saving potential of these burgeoning resources, it is critical to invest in the development of open source software tools that are capable of drawing meaningful insight from vast amounts of time series data. Results. Here we present CauseMap, the first open source implementation of convergent cross mapping (CCM), a method for establishing causality from long time series data (&25 observations). Compared to existing time series methods, CCM has the advantage of being model-free and robust to unmeasured confounding that could otherwise induce spurious associations. CCM builds on Takens’ Theorem, a well-established result from dynamical systems theory that requires only mild assumptions. This theorem allows us to reconstruct high dimensional system dy- namics using a time series of only a single variable. -
Pannexin 1 and Adipose Tissue Samantha Elizabeth Adamson Fort
Pannexin 1 and Adipose Tissue Samantha Elizabeth Adamson Fort Seybert, WV BA, Princeton University, 2006 MS, University of Virginia, 2013 A Dissertation presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Department of Pharmacology University of Virginia August, 2015 Norbert Leitinger, Ph.D. (Advisor) Doug Bayliss, Ph.D. Thurl Harris, Ph.D. Coleen McNamara, MD Bimal Desai, Ph.D. 2 Copyright Page 3 ABSTRACT Defective glucose uptake in adipocytes leads to impaired metabolic homeostasis and insulin resistance, hallmarks of type 2 diabetes. Extracellular ATP-derived nucleotides and nucleosides are important regulators of adipocyte function, but the pathway for controlled ATP release from adipocytes is unknown. Here, we investigated whether Pannexin 1 (Panx1) channels control ATP release from adipocytes and contribute to metabolic homeostasis. Our studies show that adipocytes express functional Pannexin 1 (Panx1) channels that can be activated to release ATP by known mechanisms including alpha adrenergic stimulation and caspase-mediated C-terminal cleavage during apoptosis. Further, we identify insulin as a novel activator of Panx1 channels. Pharmacologic inhibition or selective genetic deletion of Panx1 from adipocytes decreased insulin-induced glucose uptake in vitro and in vivo and exacerbated diet-induced insulin resistance in mice. In obese humans, Panx1 expression in adipose tissue is increased and correlates with the degree of insulin resistance. Although in other systems extracellular ATP has been shown to be chemotactic for immune cells such as macrophages, we observed no difference in the level of macrophage infiltration or inflammation in adipose tissue of diet- induced obese, insulin resistant AdipPanx1 KO mice, (mice in which Panx1 was selectively deleted in adipocytes).