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Yang X, Yu D, Gao F, Yang J, Chen Z, Liu J, Yang X, Li L, Zhang Y, Yan C. Integrative Analysis of Morphine-Induced Differential Circular RNAs and ceRNA Networks in the Medial Prefrontal Cortex. Mol Neurobiol 2024; 61:4602-4618. [PMID: 38109006 DOI: 10.1007/s12035-023-03859-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Circular RNAs (circRNAs) are a novel type of non-coding RNAs. Despite the fact that the functional mechanisms of most circRNAs remain unknown, emerging evidence indicates that circRNAs could sponge microRNAs (miRNAs), bind to RNA binding proteins (RBP), and even be translated into protein. Recent research has demonstrated the crucial roles played by circRNAs in neuropsychiatric disorders. The medial prefrontal cortex (mPFC) is a crucial component of drug reward circuitry and exerts top-down control over cognitive functions. However, there is currently limited knowledge about the correlation between circRNAs and morphine-associated contextual memory in the mPFC. Here, we performed morphine-induced conditioned place preference (CPP) in mice and extracted mPFC tissue for RNA-sequencing. Our study represented the first attempt to identify differentially expressed circRNAs (DEcircRNAs) and mRNAs (DEmRNAs) in the mPFC after morphine-induced CPP. We identified 47 significantly up-regulated DEcircRNAs and 429 significantly up-regulated DEmRNAs, along with 74 significantly down-regulated DEcircRNAs and 391 significantly down-regulated DEmRNAs. Functional analysis revealed that both DEcircRNAs and DEmRNAs were closely associated with neuroplasticity. To further validate the DEcircRNAs, we conducted qRT-PCR, Sanger sequencing, and RNase R digestion assays. Additionally, using an integrated bioinformatics approach, we constructed ceRNA networks and identified critical circRNA/miRNA/mRNA axes that contributed to the development of morphine-associated contextual memory. In summary, our study provided novel insights into the role of circRNAs in drug-related memory, specifically from the perspective of ceRNAs.
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Affiliation(s)
- Xixi Yang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Dongyu Yu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Feifei Gao
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Jingsi Yang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Zhennan Chen
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Junlin Liu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Xiaoyu Yang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Lanjiang Li
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Yuxiang Zhang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China.
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China.
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China.
| | - Chunxia Yan
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China.
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China.
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China.
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Dymond MK. A Membrane Biophysics Perspective on the Mechanism of Alcohol Toxicity. Chem Res Toxicol 2023. [PMID: 37186813 DOI: 10.1021/acs.chemrestox.3c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Motivations for understanding the underlying mechanisms of alcohol toxicity range from economical to toxicological and clinical. On the one hand, acute alcohol toxicity limits biofuel yields, and on the other hand, acute alcohol toxicity provides a vital defense mechanism to prevent the spread of disease. Herein the role that stored curvature elastic energy (SCE) in biological membranes might play in alcohol toxicity is discussed, for both short and long-chain alcohols. Structure-toxicity relationships for alcohols ranging from methanol to hexadecanol are collated, and estimates of alcohol toxicity per alcohol molecule in the cell membrane are made. The latter reveal a minimum toxicity value per molecule around butanol before alcohol toxicity per molecule increases to a maximum around decanol and subsequently decreases again. The impact of alcohol molecules on the lamellar to inverse hexagonal phase transition temperature (TH) is then presented and used as a metric to assess the impact of alcohol molecules on SCE. This approach suggests the nonmonotonic relationship between alcohol toxicity and chain length is consistent with SCE being a target of alcohol toxicity. Finally, in vivo evidence for SCE-driven adaptations to alcohol toxicity in the literature are discussed.
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Affiliation(s)
- Marcus K Dymond
- Chemistry Research and Enterprise Group, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, United Kingdom
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Chen J, Wang Y, Yang Z, Liu D, Jin Y, Li X, Deng Y, Wang B, Zhang Z, Ma Y. Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data. BMC Genomics 2023; 24:248. [PMID: 37165306 PMCID: PMC10170059 DOI: 10.1186/s12864-023-09358-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Real-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes. RESULTS In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log2(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct = - 0.5405 log2(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data. CONCLUSION Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.
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Affiliation(s)
- Jiao Chen
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunjian Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yao Jin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xixi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuhang Deng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Boya Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
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Abstract
Ethanol (EtOH) has effects on numerous cellular molecular targets, and alterations in synaptic function are prominent among these effects. Acute exposure to EtOH activates or inhibits the function of proteins involved in synaptic transmission, while chronic exposure often produces opposing and/or compensatory/homeostatic effects on the expression, localization, and function of these proteins. Interactions between different neurotransmitters (e.g., neuropeptide effects on release of small molecule transmitters) can also influence both acute and chronic EtOH actions. Studies in intact animals indicate that the proteins affected by EtOH also play roles in the neural actions of the drug, including acute intoxication, tolerance, dependence, and the seeking and drinking of EtOH. The present chapter is an update of our previous Lovinger and Roberto (Curr Top Behav Neurosci 13:31-86, 2013) chapter and reviews the literature describing these acute and chronic synaptic effects of EtOH with a focus on adult animals and their relevance for synaptic transmission, plasticity, and behavior.
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Affiliation(s)
- David M Lovinger
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism (NIAAA), Rockville, MD, USA
| | - Marisa Roberto
- Molecular Medicine Department, Scripps Research Institute, La Jolla, CA, USA.
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Coffman RE, Kraichely KN, Kreutzberger AJB, Kiessling V, Tamm LK, Woodbury DJ. Drunken lipid membranes, not drunken SNARE proteins, promote fusion in a model of neurotransmitter release. Front Mol Neurosci 2022; 15:1022756. [PMID: 36311016 PMCID: PMC9614348 DOI: 10.3389/fnmol.2022.1022756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022] Open
Abstract
Alcohol affects many neuronal proteins that are upstream or down-stream of synaptic vesicle fusion and neurotransmitter release. Less well studied is alcohol's effect on the fusion machinery including SNARE proteins and lipid membranes. Using a SNARE-driven fusion assay we show that fusion probability is significantly increased at 0.4% v/v (68 mM) ethanol; but not with methanol up to 10%. Ethanol appears to act directly on membrane lipids since experiments focused on protein properties [circular dichroism spectrometry, site-directed fluorescence interference contrast (sdFLIC) microscopy, and vesicle docking results] showed no significant changes up to 5% ethanol, but a protein-free fusion assay also showed increased lipid membrane fusion rates with 0.4% ethanol. These data show that the effects of high physiological doses of ethanol on SNARE-driven fusion are mediated through ethanol's interaction with the lipid bilayer of membranes and not SNARE proteins, and that methanol affects lipid membranes and SNARE proteins only at high doses.
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Affiliation(s)
- Robert E. Coffman
- Neuroscience Center, Brigham Young University, Provo, UT, United States
| | - Katelyn N. Kraichely
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA, United States
| | - Alex J. B. Kreutzberger
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA, United States
| | - Volker Kiessling
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA, United States
| | - Lukas K. Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA, United States
| | - Dixon J. Woodbury
- Neuroscience Center, Brigham Young University, Provo, UT, United States
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, United States
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Sex-Related Differences in Voluntary Alcohol Intake and mRNA Coding for Synucleins in the Brain of Adult Rats Prenatally Exposed to Alcohol. Biomedicines 2022; 10:biomedicines10092163. [PMID: 36140264 PMCID: PMC9496239 DOI: 10.3390/biomedicines10092163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/17/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Maternal alcohol consumption is one of the strong predictive factors of alcohol use and consequent abuse; however, investigations of sex differences in response to prenatal alcohol exposure (PAE) are limited. Here we compared the effects of PAE throughout gestation on alcohol preference, state anxiety and mRNA expression of presynaptic proteins α-, β- and γ-synucleins in the brain of adult (PND60) male and female Wistar rats. Total RNA was isolated from the hippocampus, midbrain and hypothalamus and mRNA levels were assessed with quantitative RT-PCR. Compared with naïve males, naïve female rats consumed more alcohol in “free choice” paradigm (10% ethanol vs. water). At the same time, PAE produced significant increase in alcohol consumption and preference in males but not in females compared to male and female naïve groups, correspondingly. We found significantly lower α-synuclein mRNA levels in the hippocampus and midbrain of females compared to males and significant decrease in α-synuclein mRNA in these brain areas in PAE males, but not in females compared to the same sex controls. These findings indicate that the impact of PAE on transcriptional regulation of synucleins may be sex-dependent, and in males’ disruption in α-synuclein mRNA expression may contribute to increased vulnerability to alcohol-associated behavior.
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Wingo TS, Liu Y, Gerasimov ES, Vattathil SM, Wynne ME, Liu J, Lori A, Faundez V, Bennett DA, Seyfried NT, Levey AI, Wingo AP. Shared mechanisms across the major psychiatric and neurodegenerative diseases. Nat Commun 2022; 13:4314. [PMID: 35882878 PMCID: PMC9325708 DOI: 10.1038/s41467-022-31873-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 07/07/2022] [Indexed: 12/14/2022] Open
Abstract
Several common psychiatric and neurodegenerative diseases share epidemiologic risk; however, whether they share pathophysiology is unclear and is the focus of our investigation. Using 25 GWAS results and LD score regression, we find eight significant genetic correlations between psychiatric and neurodegenerative diseases. We integrate the GWAS results with human brain transcriptomes (n = 888) and proteomes (n = 722) to identify cis- and trans- transcripts and proteins that are consistent with a pleiotropic or causal role in each disease, referred to as causal proteins for brevity. Within each disease group, we find many distinct and shared causal proteins. Remarkably, 30% (13 of 42) of the neurodegenerative disease causal proteins are shared with psychiatric disorders. Furthermore, we find 2.6-fold more protein-protein interactions among the psychiatric and neurodegenerative causal proteins than expected by chance. Together, our findings suggest these psychiatric and neurodegenerative diseases have shared genetic and molecular pathophysiology, which has important ramifications for early treatment and therapeutic development.
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Affiliation(s)
- Thomas S Wingo
- Goizueta Alzheimer's Disease Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Yue Liu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Selina M Vattathil
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Meghan E Wynne
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jiaqi Liu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Adriana Lori
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
| | - Victor Faundez
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Goizueta Alzheimer's Disease Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Aliza P Wingo
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA.
- Veterans Affairs Atlanta Health Care System, Decatur, GA, USA.
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Ghosh A, Muthuraju S, Badal S, Wooden J, Leasure JL, Roman G, Das J. Differential Expression of Presynaptic Munc13-1 and Munc13-2 in Mouse Hippocampus Following Ethanol Drinking. Neuroscience 2022; 487:166-183. [PMID: 35167938 PMCID: PMC8930510 DOI: 10.1016/j.neuroscience.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/22/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
Abstract
The Munc13 family of proteins is critically involved in synaptic vesicle priming and release in glutamatergic neurons in the brain. Munc13-1 binds to alcohol and, in Drosophila, modulates sedation sensitivity and self-administration. We examined the effect of alcohol consumption on the expression of Munc13-1 and Munc13-2, NMDA receptor subunits GluN1, GluN2A and GluN2B in the hippocampus-derived HT22 cells, hippocampal primary neuron culture, and wild-type and Munc13-1+/- male mouse hippocampus after ethanol consumption (Drinking in the Dark (DID) paradigm). In HT22 cells, Munc13-1 was upregulated following 25 mM ethanol treatment for 24 h. In the primary neuronal culture, however, the expression of both Munc13-1 and Munc13-2 increased after ethanol exposure. While Munc13-1 was upregulated in the hippocampus, Munc13-2 was downregulated following DID. This differential effect was found in the CA1 subfield of the hippocampus. Although Munc13-1+/- mice had approximately 50% Munc13-1 expression compared to wild-type, it was nonetheless significantly increased following DID. Munc13-1 and Munc13-2 were expressed in vesicular glutamate transporter1 (VGLUT1) immunoreactive neurons in the hippocampus, but ethanol did not alter the expression of VGLUT1. The NMDA receptor subunits, GluN1, GluN2A and GluN2B were upregulated in the hippocampal primary culture and in the CA1. Ethanol exerts a differential effect on the expression of Munc13-1 and Munc13-2 in the CA1 in male mice. Our study also found that ethanol's effect on Munc13 expression is dependent on the experimental paradigm, and both Munc13-1 and Munc13-2 could contribute to the ethanol-induced augmentation of glutamatergic neurotransmission.
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Affiliation(s)
- Anamitra Ghosh
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, United States
| | - Sangu Muthuraju
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, United States
| | - Sean Badal
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, United States
| | - Jessica Wooden
- Department of Psychology, University of Houston, Houston, TX 77204, United States
| | - J Leigh Leasure
- Department of Psychology, University of Houston, Houston, TX 77204, United States
| | - Gregg Roman
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677, United States
| | - Joydip Das
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, United States.
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