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Labib D, Wang Z, Prakash P, Zimmer M, Smith MD, Frazel PW, Barbar L, Sapar ML, Calabresi PA, Peng J, Liddelow SA, Fossati V. Proteomic Alterations and Novel Markers of Neurotoxic Reactive Astrocytes in Human Induced Pluripotent Stem Cell Models. Front Mol Neurosci 2022; 15:870085. [PMID: 35592112 PMCID: PMC9113221 DOI: 10.3389/fnmol.2022.870085] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/29/2022] [Indexed: 12/20/2022] Open
Abstract
Astrocytes respond to injury, infection, and inflammation in the central nervous system by acquiring reactive states in which they may become dysfunctional and contribute to disease pathology. A sub-state of reactive astrocytes induced by proinflammatory factors TNF, IL-1α, and C1q ("TIC") has been implicated in many neurodegenerative diseases as a source of neurotoxicity. Here, we used an established human induced pluripotent stem cell (hiPSC) model to investigate the surface marker profile and proteome of TIC-induced reactive astrocytes. We propose VCAM1, BST2, ICOSL, HLA-E, PD-L1, and PDPN as putative, novel markers of this reactive sub-state. We found that several of these markers colocalize with GFAP+ cells in post-mortem samples from people with Alzheimer's disease. Moreover, our whole-cells proteomic analysis of TIC-induced reactive astrocytes identified proteins and related pathways primarily linked to potential engagement with peripheral immune cells. Taken together, our findings will serve as new tools to purify reactive astrocyte subtypes and to further explore their involvement in immune responses associated with injury and disease.
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Affiliation(s)
- David Labib
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
| | - Zhen Wang
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Priya Prakash
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, United States
| | - Matthew Zimmer
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
| | - Matthew D. Smith
- Department of Neurology, Johns Hopkins University, Baltimore, MD, United States
| | - Paul W. Frazel
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, United States
| | - Lilianne Barbar
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
| | - Maria L. Sapar
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
| | - Peter A. Calabresi
- Department of Neurology, Johns Hopkins University, Baltimore, MD, United States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, United States
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Shane A. Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, United States
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, NY, United States
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, United States
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY, United States
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
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Ji H, Sapar ML, Sarkar A, Wang B, Han C. Phagocytosis and self-destruction break down dendrites of Drosophila sensory neurons at distinct steps of Wallerian degeneration. Proc Natl Acad Sci U S A 2022; 119:e2111818119. [PMID: 35058357 PMCID: PMC8795528 DOI: 10.1073/pnas.2111818119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
After injury, severed dendrites and axons expose the "eat-me" signal phosphatidylserine (PS) on their surface while they break down. The degeneration of injured axons is controlled by a conserved Wallerian degeneration (WD) pathway, which is thought to activate neurite self-destruction through Sarm-mediated nicotinamide adenine dinucleotide (NAD+) depletion. While neurite PS exposure is known to be affected by genetic manipulations of NAD+, how the WD pathway coordinates both neurite PS exposure and self-destruction and whether PS-induced phagocytosis contributes to neurite breakdown in vivo remain unknown. Here, we show that in Drosophila sensory dendrites, PS exposure and self-destruction are two sequential steps of WD resulting from Sarm activation. Surprisingly, phagocytosis is the main driver of dendrite degeneration induced by both genetic NAD+ disruptions and injury. However, unlike neuronal Nmnat loss, which triggers PS exposure only and results in phagocytosis-dependent dendrite degeneration, injury activates both PS exposure and self-destruction as two redundant means of dendrite degeneration. Furthermore, the axon-death factor Axed is only partially required for self-destruction of injured dendrites, acting in parallel with PS-induced phagocytosis. Lastly, injured dendrites exhibit a unique rhythmic calcium-flashing that correlates with WD. Therefore, both NAD+-related general mechanisms and dendrite-specific programs govern PS exposure and self-destruction in injury-induced dendrite degeneration in vivo.
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Affiliation(s)
- Hui Ji
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Maria L Sapar
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Ankita Sarkar
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Chun Han
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853;
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
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Sapar ML, Ji H, Wang B, Poe AR, Dubey K, Ren X, Ni JQ, Han C. Phosphatidylserine Externalization Results from and Causes Neurite Degeneration in Drosophila. Cell Rep 2020; 24:2273-2286. [PMID: 30157423 PMCID: PMC6174084 DOI: 10.1016/j.celrep.2018.07.095] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/25/2018] [Accepted: 07/27/2018] [Indexed: 01/20/2023] Open
Abstract
Phagocytic clearance of degenerating dendrites or axons is critical for maintaining tissue homeostasis and preventing neuroinflammation. Externalized phosphatidylserine (PS) has been postulated to be an ‘‘eat-me’’ signal allowing recognition of degenerating neurites by phagocytes. Here we show that in Drosophila, PS is dynamically exposed on degenerating dendrites during developmental pruning and after physical injury, but PS exposure is suppressed when dendrite degeneration is genetically blocked. Ectopic PS exposure via phospholipid flippase knockout and scramblase overexpression induced PS exposure preferentially at distal dendrites and caused distinct modes of neurite loss that differ in larval sensory dendrites and in adult olfactory axons. Surprisingly, extracellular lactadherin that lacks the integrin-interaction domain induced phagocyte-dependent degeneration of PS-exposing dendrites, revealing an unidentified bridging function that potentiates phagocytes. Our findings establish a direct causal relationship between PS exposure and neurite degeneration in vivo. Using in vivo phosphatidylserine (PS) sensors, Sapar et al. reveal dynamic patterns of PS exposure on degenerating dendrites in Drosophila. Flippase knockout and scramblase overexpression lead to ectopic PS exposure on distal dendrites and context-dependent neurite degeneration. Lactadherin potentiates phagocytes to destruct PS-exposing dendrites, independent of its integrin-interaction domain.
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Affiliation(s)
- Maria L Sapar
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Hui Ji
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amy R Poe
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Kush Dubey
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Xingjie Ren
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chun Han
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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Sapar ML, Han C. Die in pieces: How Drosophila sheds light on neurite degeneration and clearance. J Genet Genomics 2019; 46:187-199. [PMID: 31080046 DOI: 10.1016/j.jgg.2019.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/24/2019] [Accepted: 03/26/2019] [Indexed: 01/08/2023]
Abstract
Dendrites and axons are delicate neuronal membrane extensions that undergo degeneration after physical injuries. In neurodegenerative diseases, they often degenerate prior to neuronal death. Understanding the mechanisms of neurite degeneration has been an intense focus of neurobiology research in the last two decades. As a result, many discoveries have been made in the molecular pathways that lead to neurite degeneration and the cell-cell interactions responsible for the subsequent clearance of neuronal debris. Drosophila melanogaster has served as a prime in vivo model system for identifying and characterizing the key molecular players in neurite degeneration, thanks to its genetic tractability and easy access to its nervous system. The knowledge learned in the fly provided targets and fuel for studies in other model systems that have further enhanced our understanding of neurodegeneration. In this review, we will introduce the experimental systems developed in Drosophila to investigate injury-induced neurite degeneration, and then discuss the biological pathways that drive degeneration. We will also cover what is known about the mechanisms of how phagocytes recognize and clear degenerating neurites, and how recent findings in this area enhance our understanding of neurodegenerative disease pathology.
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Affiliation(s)
- Maria L Sapar
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Chun Han
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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Poe AR, Wang B, Sapar ML, Ji H, Li K, Onabajo T, Fazliyeva R, Gibbs M, Qiu Y, Hu Y, Han C. Robust CRISPR/Cas9-Mediated Tissue-Specific Mutagenesis Reveals Gene Redundancy and Perdurance in Drosophila. Genetics 2019; 211:459-472. [PMID: 30504366 PMCID: PMC6366929 DOI: 10.1534/genetics.118.301736] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022] Open
Abstract
Tissue-specific loss-of-function (LOF) analysis is essential for characterizing gene function. Here, we present a simple, yet highly efficient, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated tissue-restricted mutagenesis (CRISPR-TRiM) method for ablating gene function in Drosophila This binary system consists of a tissue-specific Cas9 and a ubiquitously expressed multi-guide RNA (gRNA) transgene. We describe convenient toolkits for making enhancer-driven Cas9 lines and multi-gRNAs that are optimized for mutagenizing somatic cells. We demonstrate that insertions or deletions in coding sequences more reliably cause somatic mutations than DNA excisions induced by two gRNAs. We further show that enhancer-driven Cas9 is less cytotoxic yet results in more complete LOF than Gal4-driven Cas9 in larval sensory neurons. Finally, CRISPR-TRiM efficiently unmasks redundant soluble N-ethylmaleimide-sensitive factor attachment protein receptor gene functions in neurons and epidermal cells. Importantly, Cas9 transgenes expressed at different times in the neuronal lineage reveal the extent to which gene products persist in cells after tissue-specific gene knockout. These CRISPR tools can be applied to analyze tissue-specific gene function in many biological processes.
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Affiliation(s)
- Amy R Poe
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Bei Wang
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Maria L Sapar
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Hui Ji
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Kailyn Li
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Tireniolu Onabajo
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Rushaniya Fazliyeva
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Mary Gibbs
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Yue Qiu
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Yuzhao Hu
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Chun Han
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
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Higuchi-Sanabria R, Vevea JD, Charalel JK, Sapar ML, Pon LA. The transcriptional repressor Sum1p counteracts Sir2p in regulation of the actin cytoskeleton, mitochondrial quality control and replicative lifespan in Saccharomyces cerevisiae. Microb Cell 2016; 3:79-88. [PMID: 28357337 PMCID: PMC5349106 DOI: 10.15698/mic2016.02.478] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Increasing the stability or dynamics of the actin cytoskeleton can extend
lifespan in C. elegans and S. cerevisiae.
Actin cables of budding yeast, bundles of actin filaments that mediate cargo
transport, affect lifespan control through effects on mitochondrial quality
control. Sir2p, the founding member of the Sirtuin family of lifespan
regulators, also affects actin cable dynamics, assembly, and function in
mitochondrial quality control. Here, we obtained evidence for novel interactions
between Sir2p and Sum1p, a transcriptional repressor that was originally
identified through mutations that genetically suppress sir2∆
phenotypes unrelated to lifespan. We find that deletion of SUM1
in wild-type cells results in increased mitochondrial function and actin cable
abundance. Furthermore, deletion of SUM1 suppresses defects in
actin cables and mitochondria of sir2∆ yeast, and extends the
replicative lifespan and cellular health span of sir2∆ cells.
Thus, Sum1p suppresses Sir2p function in control of specific aging determinants
and lifespan in budding yeast.
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Affiliation(s)
- Ryo Higuchi-Sanabria
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jason D Vevea
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA. ; Current address: Department of Neuroscience, University of Wisconsin, Madison, WI, USA
| | - Joseph K Charalel
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA. ; Current address: Department of Genetics, Stanford University, Stanford, CA, USA
| | - Maria L Sapar
- Department of Biological Sciences, Hunter College and The Graduate Center Biochemistry, Biology and Biopsychology and Behavioral Neuroscience Programs, CUNY, New York, NY 10065, USA. Current address: Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA. ; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
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D'Hulst C, Parvanova I, Tomoiaga D, Sapar ML, Feinstein P. Fast quantitative real-time PCR-based screening for common chromosomal aneuploidies in mouse embryonic stem cells. Stem Cell Reports 2013; 1:350-9. [PMID: 24319669 PMCID: PMC3849352 DOI: 10.1016/j.stemcr.2013.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/07/2013] [Accepted: 08/08/2013] [Indexed: 11/26/2022] Open
Abstract
Chromosomal integrity has been known for many years to affect the ability of mouse embryonic stem cells (mESCs) to contribute to the germline of chimeric mice. Abnormal chromosomes are generally detected by standard cytogenetic karyotyping. However, this method is expensive, time consuming, and often omitted prior to blastocyst injection, consequently reducing the frequency of mESC-derived offspring. Here, we show a fast, accurate, and inexpensive screen for identifying the two most common aneuploidies (Trisomy 8 and loss of chromosome Y) in genetically manipulated mESCs using quantitative real-time PCR (qPCR). Screening against these two aneuploidies significantly increases the fraction of normal mESC clones. Our method is extremely sensitive and can detect as low as 10% aneuploidy among a large population of mESCs. It greatly expedites the generation of mutant mice and provides a quick tool for assessing the aneuploidy percentages of any mESC line. Fast aneuploidy detection of mESCs using quantitative real-time PCR Simultaneous processing of multiple cell lines Highly sensitive: identifies low percentage of aneuploidy within an ESC clone Method can detect loss or gain of any chromosomal region of interest
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Affiliation(s)
- Charlotte D'Hulst
- Department of Biological Sciences, Hunter College and The Graduate Center Biochemistry, Biology and Biopsychology and Behavioral Neuroscience Programs, The City University of New York, New York, NY 10065, USA
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Bubnell J, Pfister P, Sapar ML, Rogers ME, Feinstein P. β2 adrenergic receptor fluorescent protein fusions traffic to the plasma membrane and retain functionality. PLoS One 2013; 8:e74941. [PMID: 24086401 PMCID: PMC3781101 DOI: 10.1371/journal.pone.0074941] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 08/07/2013] [Indexed: 11/29/2022] Open
Abstract
Green fluorescent protein (GFP) has proven useful for the study of protein interactions and dynamics for the last twenty years. A variety of new fluorescent proteins have been developed that expand the use of available excitation spectra. We have undertaken an analysis of seven of the most useful fluorescent proteins (XFPs), Cerulean (and mCerulean3), Teal, GFP, Venus, mCherry and TagRFP657, as fusions to the archetypal G-protein coupled receptor, the β2 adrenergic receptor (β2AR). We have characterized these β2AR::XFP fusions in respect to membrane trafficking and G-protein activation. We noticed that in the mouse neural cell line, OP 6, that membrane bound β2AR::XFP fusions robustly localized in the filopodia identical to gap::XFP fusions. All β2AR::XFP fusions show responses indistinguishable from each other and the non-fused form after isoprenaline exposure. Our results provide a platform by which G-protein coupled receptors can be dissected for their functionality.
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Affiliation(s)
- Jaclyn Bubnell
- Department of Biological Sciences, Hunter College and The Graduate Center Biochemistry, Biology and Biopsychology and Behavioral Neuroscience Programs, CUNY, New York, New York, United States of America
| | - Patrick Pfister
- Corporate Research and Development, Firmenich Inc., Plainsboro, New Jersey, United States of America
| | - Maria L. Sapar
- Department of Biological Sciences, Hunter College and The Graduate Center Biochemistry, Biology and Biopsychology and Behavioral Neuroscience Programs, CUNY, New York, New York, United States of America
| | - Matthew E. Rogers
- Corporate Research and Development, Firmenich Inc., Plainsboro, New Jersey, United States of America
| | - Paul Feinstein
- Department of Biological Sciences, Hunter College and The Graduate Center Biochemistry, Biology and Biopsychology and Behavioral Neuroscience Programs, CUNY, New York, New York, United States of America
- * E-mail:
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