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Adv Cell Bio Chapter 16 Notes!

by: Izabella Nill Gomez

Adv Cell Bio Chapter 16 Notes! BCMB 311

Marketplace > University of Tennessee - Knoxville > BCMB 311 > Adv Cell Bio Chapter 16 Notes
Izabella Nill Gomez
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Hey guys! So chapter 16 from Dr. Park is finally uploaded! It includes notes from lecture as well as the textbook, detailed and vocab based! Enjoy!
Advanced Cellular Biology
Dr. Barry Bruce, Dr. J. Park
Class Notes
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This 10 page Class Notes was uploaded by Izabella Nill Gomez on Friday April 15, 2016. The Class Notes belongs to BCMB 311 at University of Tennessee - Knoxville taught by Dr. Barry Bruce, Dr. J. Park in Spring 2016. Since its upload, it has received 6 views.


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Date Created: 04/15/16
Advanced Cell Bio Chapter 16 Notes: In signaling between cells, signaling cell produces a type of extracellular signal molecule detected by a target cell. Target cells have proteins (receptors) that recognize and respond specifically to the signal molecule. Signal transduction begins when the receptor on the target cell receives an incoming extracellular signal and converts it to intracellular signaling molecules that alter cell behavior. Signal molecules in multicellular organisms can be proteins, peptides, amino acids, nucleotides, steroids, fatty acids, etc.--they rely on a handful of styles to get the message across. In cells, the most public style of cell to cell communication is broadcasting through the whole body via the bloodstream/sap. Extracellular signal molecules used like this are hormones--in animals, they are produced by the endocrine cells (ex: part of the pancreas has the endocrine glands (including insulin). Less public is paracrine signaling--signal molecules diffuse locally through the extracellular fluid, remaining in neighborhood of the cell that secretes. Act as local mediators on nearby cells (ex: regulation of inflammation; cell proliferation in a healing wound). In some cases, cells respond to the local mediators they produce-- autocrine signaling--ex: cancer cells. In neuronal signaling, nerve cells deliver messages over long distances. The message is delivered quickly and specifically to individual target cells through private cells. Signals reaching an axon terminal are electrical signals that are converted to chemical through signal molecule neurotransmitter--diffuses across the synapse and is taken back up as an electrical signal again. Most intimate and short- range communication does not use secretion of a molecule--uses physical contact through signal molecules lodged in the plasma membrane of signaling cell and receptor proteins of the target cell (contact dependent). Whether a cell responds to a signal molecule depends on whether it possesses a receptor for that signal. Each receptor is usually activated by only one type of signal--without appropriate receptor, the cell will not respond. Limited set of receptors produced to restrict types of signals that can affect it. Restricted set of extracellular signals can affect the behavior of the target cell in different ways. Can alter shape, movement, metabolism or gene expression, or a combination. Signal from a cell surface receptor is generally conveyed to the target cell interior via intracellular signaling molecules that act in sequence and alter the activity of effector proteins--those have direct effect on the behavior of the target cell. Intracellular relay system and effector proteins on which it acts vary from one specialized cell to the next, so different cells respond to the same signal in different ways. Ex: heart pacemaker cell, salivary gland and skeletal muscle react to acetylcholine differently (pacemaker and salivary have the same receptors). Information conveyed by the signal depends on how the cell receives and interprets the signal. Combination of signals can evoke a response different from the sum effects that each signal would trigger on its own. “Tailoring” of the cell response occurs in part because the relay systems activated by different signals interact--the presence of one signal will modify the effects of the other. One combination can drive the cell to survive, differentiate, grow and divide or die (without signals). Rapid responses to cell signaling arise from activity of proteins that are already present inside the target cell. Slower responses arise from having to make the protein from scratch. Extracellular signal molecules fall into 2 classes--first and targets has molecules too large/hydrophobic to cross the plasma membrane of the target cell. Rely on receptors on the surface of the target cell to relay the message across the membrane. Second class consists of molecules small enough or hydrophobic enough to pass through the plasma membrane and into the cytosol. Once inside, it activates intracellular enzymes or bind to intracellular receptor proteins that regulate gene expression. One important category of signal molecule that relies on intracellular receptors is steroid hormones--including cortisol, steroid, estradiol and thyroid hormone thyroxine. All pass through the plasma of the target and bind to receptors in the cytosol or nucleus. Both called nuclear receptors because when activate by hormone binding, they act as transcription regulators in the nucleus. In unstimulated cells, nuclear receptors are inactive--when bound to a hormone, change conformation that activates, allowing promotion/inhibition of transcription at specific target genes. Each hormone binds to a different nuclear receptor and each acts at a different set of regulatory sites in DNA. A given hormone regulates different sets of genes in different cell types--evoking different responses. Lack of nuclear receptors and hormones has dramatic consequences (like androgen insensitivity (XY without testosterone receptors)). Some dissolved gasses can diffuse across the membrane to the cell interior and directly regulate the activity of specific intracellular proteins. The direct approach allows signals to alter a target cell within a few seconds/minutes. Nitric oxide (NO) acts like this. Synthesis from amino acid arginine and diffuses to neighboring cells. Gas acts locally because it is quickly converted to nitrites/ates by reacting with O2 and H2O outside cells. Endothelial cells (line the blood vessels) release NO in response to neurotransmitters by nerve endings, allows smooth muscles cells in adjacent Bessel wall to relax and dilate, increasing blood flow. Effect of NO accounts for action of nitroglycerine, used for hundreds of yeas to treat heart angia. Nitroglycerine to NO relaxes vessels and decreases heart workload. NO is also used by nerves to signal neighboring cells for infections. Inside target cells, NO binds and activates guanylyl cyclase to form CGMP from GTP. cGMP is a signaling molecules to link NO to the ultimate response. Viagra inhibits degradation of cGMP by an enzyme. In contrast to NO and steroid hormones, the cast majority of signal molecules are too large or hydrophobic to cross the plasma membrane. Bind to cell-surface receptor proteins that span the plasma membrane. Transmembrane receptors detect a signal outside and relay a message in new form across the membrane to interior of the cell. Receptor performs primary step in signal transduction-- recognizes extracellular signal and generates new intracellular signals in response. Resulting signals work like a relay race--message is passed downstream from one intracellular signaling molecule to another, each activating/generating the next signaling molecule in the pathway until a metabolic enzyme is kicked into action, cytosol tweaked to new configuration, or a gene is switched on/off. Final outcome is the response of the cell. Components of intracellular signaling pathways perform one or more crucial functions: 1. Relay signal onward and spread through cell 2. Amplify signal received, making stronger so a few extracellular signal molecules are enough to evoke a large intracellular response 3. Detect signals from more than one intracellular signaling pathway and integrate them before relaying the signal onward. 4. Distribute the signal to more than one effector protein, creating branches in the information flow diagram and evoking a complex response. Steps in signaling pathway are generally subject to modulation by feedback regulation. In positive feedback, component that lies downstream in the pathway acts on an earlier component in the same pathway to enhance the response to the initial signal; in negative feedback, downstream component acts to inhibit an earlier component in the pathway to diminish the response to the initial signal. Positive feedback can be all or none switch-like responses, negative can generate responses that oscillate on and off. Many key intracellular signaling proteins behave as molecular switches, receipt of a signal causes them to toggle between inactive/active state. Once activated, can stimulate or suppress other proteins in the signaling pathway. Persist until another process turns it off. Importance of switching-off process important for recovery and preparation for another signal transmission--all receptors must be rest for inactivated state/unstimulated state. Proteins that act as molecular switches have two classes-- first and largest consists of proteins activated by phosphorylation-switch thrown in one direction by protein kinase, which covalently attaches a P group onto the switch protein, and other direction by protein phosphatase, which removes P. Activity of any protein regulated by phosphorylation depends moment by moment on the balance between activities of protein kinases that phosphorylates and phosphatases that de-phosphorylate. Many switch proteins controlled by phosphorylation are protein kinases organized into phosphorylation cascades: one kinase, activated, phosphorylates the next in sequence and so on, transmitting the signal onward and amplifying, distributing, regulating it. Two types for intracellular pathways: serine/threonine kinases (phosphorylate proteins on threonine/serine) and tyrosine kinases (phosphorylate proteins on tyrosines). Other class of switch proteins in the intracellular signaling pathway are GTP binding proteins--toggle between active/inactive depending on whether GTP/GDP bound. Once activated by GTP, the proteins have intrinsic GTPase activity and must shut themselves off by hydrolyzing GTP-bound to GDP. Two types for intracellular--large trimeric GTP binding proteins (G proteins) relay messages from G-protein coupled receptors. Other cell surface receptors rely on small monomeric GTPases to help relay signals--aided by 2 sets of regulatory proteins--guanine nucleotide exchange factors (GEFs) activate switch proteins by promoting exchange of GDP for GTP, and GTPase-activating proteins (GAPs) turn them off by promoting GTP hydrolysis. All cell-surface receptors bind to extracellular signal molecules and transduce their message into one or more intracellular signaling molecules that alter the cell’s behavior. Most of these receptors belong to 3 large classes that differ in the transduction mechanism they use. Ion channel-coupled receptors change permeability of the plasma membrane to selected ions, altering membrane potential and producing electrical current. G-protein coupled receptors activate membrane bound trimeric G-proteins which then activate (or inhibit) an enzyme/ion channel in the plasma membrane, initiating an intracellular signaling cascade. Enzyme-coupled receptors either act as enzymes or associate with enzymes inside the cell; when stimulated, the enzymes can activated a variety of intracellular signaling pathways. A number of different types of receptors in these classes are greater than the number of extracellular signals that act on them. Because for many extracellular signal molecules there is more than one type of receptor, and can belong to different receptor classes. Acetylcholine (neurotransmitter) acts on skeletal muscle cells via ion channel-coupled receptor, where in heart cell it acts through a G protein-coupled receptor. The two receptors generate different intracellular signals and enable two types of cells to react to acetylcholine in different ways, increasing contractions in muscle cells or decreasing heart rate in heart pacemaker cells. Plethora of cell-surface receptors allows for targets for many foreign substances that interfere with physiology, like heroin/nicotine to tranquilizers and chili peppers that block/overstimulate receptors. Ion channel coupled receptors (transmitter-gated channels) function in the simplest/most direct way. Responsible for rapid transmission across synapses in the nervous system. G protein-coupled receptors (GPCRs) form the largest family of cell surface receptors. More than 700 GPCRs exist in humans, and mice have 1000 related to the sense of smell alone. These mediate responses to a diversity of extracellular signal molecules, including hormones, local mediators, neurotransmitters. Signal molecules are as varied in structure as function. Can be proteins, small peptides, or derivatives of amino acids or fatty acids, and for each there is a different receptor or set of. Because GPCRs are involved in such a large variety of cell processes, they are an attractive target for development of drugs to treat many disorders. 1/3 of drugs work through GPCRs. All GPCRs have a similar structure. Each made of a single polypeptide chain that threads back and forth across the lipid bilayer seven times. Super family of 7-pass transmembrane receptor proteins includes rhodopsin, olfactory receptors in vertebrate nose, receptors in mating of single cell yeasts-- GPCRs are ancient--even prokarya have structurally similar membrane proteins (ex: bacteriorhodopsin). When an extracellular signal molecule binds to GPCR, receptor protein undergoes conformational change that enables it to activate a G-protein on the other side of the plasma membrane. Several varieties of G proteins. Each is specific for a particular set of receptors and for a particular set of target enzymes or ion channels in the plasma membrane. All G proteins have a similar general structure and operate similarly. Composed of 3 subunits: alpha, beta and gamma--2 are tethered to the plasma by short lipid tails. In its unstimulated state, alpha has GDP bound and the G protein is idle. When an extracellular signal binds to the receptor, the altered receptor activates the G protein by causing alpha to decrease its affinity for GDP and exchanged for GTP. In some cases, it breaks up the subunits so activated alpha detaches from the beta-gamma complex which is also activated. Alpha and beta-gamma can then interact directly with target proteins in the plasma membrane, which in turn may relay the signal to other destinations in the cell. The longer the target proteins interact, the more prolonged the signal will be. Amount of time alpha and beta-gamma is switched on also determines how long a response lasts. Timing is controlled by behavior of the alpha subunit. Alpha has intrinsic GTPase activity, and eventually hydrolyzes GTP to GDP, returning the G protein to its original conformation. GTP hydrolysis usually occurs seconds after the G protein is activated. Shut off mechanism also offers many opportunities for control--or mishap. Ex: cholera induces cholera toxin in the epithelial gut--modifies the alpha subunit of the G protein called Gs (stimulates adenylyl cyclase)--prevents Gs from hydrolyzing GTP and locking it in the active state--excessive outflow of Cl- and H2O to the gut (diarrhea and dehydration). Same with whooping cough (pertussis)--colonizes in lung, produces toxin that alters the alpha subunit of Gi (inhibits adenylyl cyclase) locking the G protein into the inactive state. Target proteins recognized by G protein subunits are enzymes/ion channels in the plasma membrane. 20 different types of mammalian G proteins, each activated by a particular set of cell-surface receptors and dedicated to activating a particular set of target proteins. Binding of extracellular signal to GPCR leads to changes in activities of a specific subset of possible target proteins in the plasma membrane, leading to a response appropriate for that signal and type of cell. Direct G protein regulation of ion channels--heatbeat in animals is controlled by 2 nerves, one speeds the heart up and the other slows it down--slowing heartbeat releases acetylcholine that binds to GPCR on the surface of pacemaker cells-- activates G protein Gi--beta-gamma complex binds to the intracellular face of the K+ channel in the plasma membrane, forcing it open--slows the heart by preventing electrical activity. K+ channel recloses when 2 subunits inactivates by hydrolyzing GTP. When the G proteins interact with ion channels, it causes an immediate change in state/behavior of the cell--interaction with enzymes has slower consequences--2 frequent targets is adenylyl cyclase that produces small intracellular signaling molecules cAMP and phospholipase C--generates small intracellular signal inositol triphosphate and diaglycerol. Inositol promotes the accumulation of Ca2+00another signal molecule. Adenylyl and phospholipase C are activated by different G proteins, allowing to couple their production to different extracellular signals. Coupling may be stimulatory/inhibitory, but G proteins stimulate enzyme activity. Small intracellular signal molecules form enzymes are called small/second messengers-- first messengers are the extracellular signals that activated the enzymes--second messengers diffuse from the source, amplifying the signal. Many extracellular signals via GPCRs affect activity of adenylyl cyclase and alter intracellular concentration of the second messenger cAMP--activated G protein alpha subunit switches adenylyl on, causing a sudden increase of cAMP from ATP in the cell. Because it stimulates, this G protein is Gs. To help terminate the signal, second enzyme cAMP phosphodiesterase converts cAMP to AMP-- ex: caffeine distorts phosphodiesterase (inhibits)--blocking cAMP degradation. cAMP phosphodiesterase is continuously active, eliminates cAMP rapidly so cytosolic concentration of cAMP can change rapidly in response to extracellular signals. cAMP is water soluble, so sometimes it can carry a signal throughout the cell. cAMP exerts most effects by activating cAMP-dependent protein kinase (PKA)--normally held in inactive complex with regulatory protein. Binding of cAMP to regulatory protein forces conformational change that releases inhibition and unleashes active kinase--then catalyzes phosphorylation of serines/threonines on specific intracellular proteins, altering activity. Ex: when excited/scared, adrenal gland releases adrenaline, circulates, binds to GPCR adrenergine receptors--help prepare the body for sudden action. In muscle cells, skeletal muscle adrenaline increases cAMP to break down glycogen-- activates PKA to activate an enzyme for glycogen breakdown. Also inhibits glycogen synthesis to maximize the glucose available. Adrenaline also acts on fat cells. cAMP responses can be slow/fast--in slow, PKA typically phosphorylates transcription regulators that then activate transcription of selected genes--some GPCRs exert effect via G protein Gq, which then activates membrane bound enzyme phospholipase C instead of adenylyl--once activated phospholipase C propagates the signal by cleaving a lipid molecule that is a component of the plasma membrane--an inositol phospholipid present in small quantities in the cytosol leaflet of the membrane lipid bilayer. Because of phospholipid involvement, signaling pathway that begins with activation of phospholipase C is referred as the inositol phospholipid pathway--operates in almost all eukaryotic cells and can regulate many different effector proteins. Action of phospholipase C generates two second messengers--inositol 1,4,5-triphosphate (IP3) and diaglycerol (DAG). Both play an important role in relaying the signal. IP3 is H2O-soluble--sugar phosphate released into the cytosol--binds to and opens Ca2+ channels in the ER--Ca2+ in the ER rushes to the cytosol and causes a rise in concentration--signals other proteins. Diaglycerol is a lipid that remains embedded in the plasma membrane after being produced by phospholipase C, helps recruit and activate a protein kinase that translocates from the cytosol to the plasma membrane-- protein kinase C (PKC) because it also binds to Ca2+ to be active. Once active, PKC phosphorylates a set of intracellular proteins that varies depending on cell type--operates on the same principle as PKA but phosphorylates different proteins. When sperm fertilizes the egg cell, Ca2+ triggers egg to start development--for muscles, the signal from a nerve triggers rise in Ca2+ that initiates muscle contraction. Ca2+ concentrations are very low in the cytosol compared to the extracellular fluid and ER--actively pumped out--creates steep EG across the ER and plasma membrane. Effects of Ca2+ in the cytosol are largely indirect--mediated through interaction of Ca2+ with different kinds of Ca2+ responsive proteins. Most widespread and common is calmodulin--present in the cytosol of all eukaryotic cells that have been examined, including plants, fungi, protozoa. When Ca2+ binds to calmodulin, protein undergoes conformational change that enables to interact with a wide range of target proteins in the cell, altering activities. Important class of targets for calmodulin is Ca2+/calmodulin-dependent protein kinases (CaM-kinases)--when activated by binding to calmodulin complexed with Ca2+, it influences other processes by phosphorylating selected proteins. Signaling cascades associated with GPCRs take seconds to execute. Among the faster of all responses mediated by GPCR is to light--20 msec for cone receptors to respond-- electrical response. Cascades allow for amplification of an incoming signal and allow cells to adapt to detect signals of varying intensity. Rods are responsible for noncolor vision in dim light. Light is sensed by rhodopsin--GPC light receptor--light activated rhodopsin activates G-protein transducing--alpha subunit activates an intracellular cascade that causes Na+ cation channels to close in the plasma membrane and produce a change in voltage across the cell membrane--alters neurotransmitter release and leads to nerve impulse being sent to the brain. Signal repeatedly amplified via intracellular signaling pathway--when conditions are dim, amplification is enormous. Adaptation to bright light steps down amplification so photoreceptors are not overwhelmed--depends on negative feedback--intense response in photosynthetic cell decreases cytosolic Ca2+ concentration--inhibiting enzymes responsible for signal amplification--adaptation frequently occurs in intracellular signaling pathways that respond to extracellular signal molecules-- allowing cells to respond to fluctuations in concentration of such molecules regardless of quantity--adaptation allows to respond both to whispering/shouting messages. Enzyme-coupled receptors are transmembrane proteins that display ligand-binding domains on the outer surface of the plasma membrane. Instead of associating with G-protein, cytoplasmic domain of the receptor acts as an enzyme itself or forms a complex with another protein that acts as an enzyme. Role in responses to extracellular signal proteins (growth factors) that regulate growth, proliferation, differentiation and survival of cells in animal tissues. Most of these signal proteins function as local mediators and can act at low concentrations--responses slow (hrs) and effects may require many intracellular transduction steps that usually lead to a change in gene expression. Enzyme coupled can mediate direct, rapid reconfiguration of the cytoskeleton, changing the cell’s shape and the way it moves. Extracellular signals that induce such changes are often not diffusible signal proteins, but proteins attached to the surfaces over which the cell is crawling. Largest class of enzyme-coupled have receptors of the cytoskeletal domain that functions as a tyrosine protein kinase, which phosphorylates particular tyrosines on specific intracellular signaling proteins--receptor tyrosine kinases (RTKs)--abnormalities in these leads to the development of most cancers. To do its job, enzyme coupled has to swrich on the enzyme activity of its intracellular domain or associated enzyme when an external signal molecule binds to its extracellular domain.ECRs usually only have one transmembrane segment, which spans the lipid bilayer as an alpha helix, binding ot extracellular signal molecules causes two receptor molecules to come together in the plasma membrane, forming a dimer. Pairing brings two intracellular tails of the receptors together, activating kinase domains so each receptor tail phosphorylates the other. In RTKs, phosphorylation on specific tyrosines. Tyrosine phosphorylation then triggers the assembly of transient but elaborate intracellular signaling complex on the cytosolic tails of the receptor. Newly phosphorylated tyrosines serve as docking sites about 10/20 of the intracellular signaling proteins. Some of these become phosphorylated/activated on binding to the receptor, and then propagate the signal; others function solely as scaffolds, which couple the receptor to other signaling proteins, helping to build the active signaling complex. Docked intracellular signaling proteins have a specific interaction domain--recognizes specific phosphorylated tyrosines on the receptor tails. Other interaction domains allow intracellular signaling proteins to recognize phosphorylated lipids produced on the cytosolic side of the plasma membrane in response to certain signals. Signaling protein complexes assembled on the cytosolic tails of RTKs can transmit a signal along several routes simultaneously to many destinations in the cell, activating/coordinating numerous biochemical changes required to trigger a complex response---cell proliferation/differentiation. To help terminate a response, tyrosine is phosphorylated reversed by protein tyrosine phosphatases that remove the P groups to tyrosines of RTKs and other intracellular signal proteins in response to extracellular signaling. In some cases, activated RTKs ( and some GPCRs) are inactivated more brutally by being dragged into the cell via endocytosis and destroyed in the lysosomes. Different RTKs recruit different collections of intracellular signaling proteins, producing different effects--some components are used by most RKTs-- phospholipase (activated by GPCRs to trigger inositol pathway--small GTP-binding protein Ras). Ras is a small GTP-binding that is bound by a lipid tail to the cytosolic face of the plasma membrane--virtually all RKS activate--including platelet-derived growth factor (PDGF) receptors, which mediate cell proliferation in wound healing and nerve growth factor (NGF) receptors, play an important part in the development of certain neurons. Ras is a member of monomeric GTPases--resembles alpha subunit of G proteins and functions as a molecular switch in the same way. Cycles between two conformation states--active with GTP bound and vice versa. Interaction with Ras- GEF encourages Ras to exchange GDP for GTP--after a delay, Ras is switched off by Ras-Gap. In active state, Ras initiates a phosphorylation cascade in which serine/threonine protein kinases phosphorylation and activate one another In sequence, like dominoes--relay carries the signal from the plasma membrane to the nucleus, includes 3-protein-kinase module-MAP kinase signaling molecule. Final kinase in the chain--Map kinase. In this pathway, Map is phosphorylated and activated by Map kinase kinase, which is activated by Map kinase kinase kinase (activated by Ras). At the end of the cascade, Map kinase phosphorylates effector proteins including transcription regulators, altering the ability to control gene transcription--may trigger proliferation, survival, differentiation and depends on which other genes are active in the cell and other signals the cell receives. The mutant form of Ras is found in cancer cells--inactivated GTPase activity so it couldn’t shut itself off--30% of human cancers have Ras mutations--those that do not are still related to it. Many of the external signals that stimulate animal cells to survive and grow act through RTKs, include insulin like growth factor (IGF) family--one important pathway that RTKs activate to promote cell growth and survival relies on enzyme phosphoinositide 3-kinase (PI3 kinase)--phosphorylates inositol phospholipids in the plasma membrane--then serve as docking sites for specific intracellular signaling proteins that relocate from the cytosol to the plasma membrane, where they can activate one another--one of the most important is serine/threonine protein kinase (Akt). Akt/protein kinase B (PKB) promotes growth and survival of many cell types by inactivating signaling proteins it phosphorylates. Inactivates cytosolic protein Bad (in active state, encourages cell into apoptosis). Phosphorylation by Akt promotes cell survival by inactivating it. PI3- kinase-Akt signaling pathway stimulates cell to grow in size, by indirectly activating serine/threonine kinase Tor. Tor stimulates cells to grow by enhancing the protein synthesis and inhibiting protein degradation. Rapamycin works by inactivating Tor (for cancers). Notch crucial receptor in all animals for development and in adults, controls development of neural cells in Drosophila--receptor acts as transcription regulator-- when activated by binding of Delta--transmembrane signal protein on the surface of a neighboring cell, Notch receptor is cleaved. Cleavage releases cytosolic tail of receptor that is then free to move to the nucleus where it helps to activate the appropriate set of Notch-responsive genes.


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