1
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Song R, Zhang J, Perszyk RE, Camp CR, Tang W, Kannan V, Li J, Xu Y, Chen J, Li Y, Liang SH, Traynelis SF, Yuan H. Differential responses of disease-related GRIN variants located in pore-forming M2 domain of N-methyl-D-aspartate receptor to FDA-approved inhibitors. J Neurochem 2023:10.1111/jnc.15942. [PMID: 37649269 PMCID: PMC10902181 DOI: 10.1111/jnc.15942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023]
Abstract
N-methyl-D-aspartate receptors (NMDAR), ionotropic glutamate receptors, mediate a slow component of excitatory synaptic transmission in the central nervous system and play a key role in normal brain function and development. Genetic variations in GRIN genes encoding NMDAR subunits that alter the receptor's functional characteristics are associated with a wide range of neurological and neuropsychiatric conditions. Pathological GRIN variants located in the M2 re-entrant loop lining the channel pore cause significant functional changes, the most consequential alteration being a reduction in voltage-dependent Mg2+ inhibition. Voltage-dependent Mg2+ block is a unique feature of NMDAR biology whereby channel activation requires both ligand binding and postsynaptic membrane depolarization. Thus, loss of NMDAR Mg2+ block will have a profound impact on synaptic function and plasticity. Here, we choose 11 missense variants within the GRIN1, GRIN2A, and GRIN2B genes that alter residues located in the M2 loop and significantly reduce Mg2+ inhibition. Each variant was evaluated for tolerance to genetic variation using the 3-dimensional structure and assessed for functional rescue pharmacology via electrophysiological recordings. Three FDA-approved NMDAR drugs-memantine, dextromethorphan, and ketamine-were chosen based on their ability to bind near the M2 re-entrant loop, potentially rectifying dysregulated NMDAR function by supplementing the reduced voltage-dependent Mg2+ block. These results provide insight of structural determinants of FDA-approved NMDAR drugs at their binding sites in the channel pore and may further define conditions necessary for the use of such agents as potential rescue pharmacology.
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Affiliation(s)
- Rui Song
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jin Zhang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Riley E Perszyk
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Chad R Camp
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Weiting Tang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Varun Kannan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jia Li
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yuchen Xu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jiahui Chen
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yinlong Li
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Steven H Liang
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Stephen F Traynelis
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Hongjie Yuan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, Georgia, USA
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2
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Aljaloud K, Aladadi YT, Alkanhal MAS, Abdulkawi WM, Hussain R. A Wideband GRIN Dielectric Lens Antenna for 5G Applications. Micromachines (Basel) 2023; 14:mi14050997. [PMID: 37241621 DOI: 10.3390/mi14050997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023]
Abstract
This paper proposes a graded effective refractive indexes (GRIN) dielectric lens for 5G applications. The inhomogeneous holes in the dielectric plate are perforated to provide GRIN in the proposed lens. The constructed lens employs a collection of slabs that correspond to the specified graded effective refractive index. The thickness and the whole lens dimensions are optimized based on designing a compact lens with optimum lens antenna performance (impedance matching bandwidth, gain, 3 dB beamwidth, and sidelobe level). A wideband (WB) microstrip patch antenna is designed to be operated over the entire band of interest from 26 GHz to 30.5 GHz. For the 5G mm-wave band of operation, the behavior of the proposed lens along with a microstrip patch antenna is analyzed at 28 GHz for various performance parameters, including impedance matching bandwidth, 3 dB beamwidth, maximum gain, and sidelobe level. It has been observed that the antenna exhibits good performance over the entire band of interest in terms of gain, 3 dB beamwidth, and sidelobe level. The numerical simulation results are validated using two different simulation solvers. The proposed unique and innovative configuration is well-suited for 5G high gain antenna solutions with a low-cost and lightweight antenna structure.
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Affiliation(s)
- Khaled Aljaloud
- Department of Electrical Engineering, King Saud University, Riyadh 11421, Saudi Arabia
| | - Yosef T Aladadi
- Department of Electrical Engineering, King Saud University, Riyadh 11421, Saudi Arabia
| | - Majeed A S Alkanhal
- Department of Electrical Engineering, King Saud University, Riyadh 11421, Saudi Arabia
| | - Wazie M Abdulkawi
- Department of Electrical Engineering, King Saud University, Riyadh 11421, Saudi Arabia
| | - Rifaqat Hussain
- Department of Electrical Engineering, King Saud University, Riyadh 11421, Saudi Arabia
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3
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Xie L, McDaniel MJ, Perszyk RE, Kim S, Cappuccio G, Shapiro KA, Muñoz-Cabello B, Sanchez-Lara PA, Grand K, Zhang J, Nocilla KA, Sheikh R, Armengol L, Romano R, Pierson TM, Yuan H, Myers SJ, Traynelis SF. Functional effects of disease-associated variants reveal that the S1-M1 linker of the NMDA receptor critically controls channel opening. Cell Mol Life Sci 2023; 80:110. [PMID: 37000222 PMCID: PMC10641759 DOI: 10.1007/s00018-023-04705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/10/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 04/01/2023]
Abstract
The short pre-M1 helix within the S1-M1 linker (also referred to as the pre-M1 linker) between the agonist-binding domain (ABD, S1) and the M1 transmembrane helix of the NMDA receptor (NMDAR) is devoid of missense variants within the healthy population but is a locus for de novo pathogenic variants associated with neurological disorders. Several de novo variants within this helix have been identified in patients presenting early in life with intellectual disability, developmental delay, and/or epilepsy. In this study, we evaluated functional properties for twenty variants within the pre-M1 linker in GRIN1, GRIN2A, and GRIN2B genes, including six novel missense variants. The effects of pre-M1 variants on agonist potency, sensitivity to endogenous allosteric modulators, response time course, channel open probability, and surface expression were assessed. Our data indicated that virtually all of the variants evaluated altered channel function, and multiple variants had profound functional consequences, which may contribute to the neurological conditions in the patients harboring the variants in this region. These data strongly suggest that the residues within the pre-M1 helix play a key role in channel gating and are highly intolerant to genetic variation.
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Affiliation(s)
- Lingling Xie
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA, 30322, USA
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Miranda J McDaniel
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA, 30322, USA
| | - Riley E Perszyk
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA, 30322, USA
| | - Sukhan Kim
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA, 30322, USA
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Gerarda Cappuccio
- Section of Pediatrics, Department of Translational Medicine, Federico II University, Via Pansini 5, 80131, Naples, Italy
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Kevin A Shapiro
- Department of Neurology, University of California, UCSF Memory and Aging Center, Sandler Neurosciences Center, San Francisco, CA, USA
| | | | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Jing Zhang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA, 30322, USA
| | - Kelsey A Nocilla
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA, 30322, USA
| | - Rehan Sheikh
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA, 30322, USA
| | - Lluis Armengol
- Quantitative Genomic Medicine Laboratories, SL (qGenomics), Barcelona, Spain
| | - Roberta Romano
- Section of Pediatrics, Department of Translational Medicine, Federico II University, Via Pansini 5, 80131, Naples, Italy
| | - Tyler Mark Pierson
- Division of Pediatric Neurology, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, USA
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, USA
- Center for the Undiagnosed Patient, Cedars-Sinai Medical Center, Los Angeles, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Hongjie Yuan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA, 30322, USA
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Scott J Myers
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA, 30322, USA
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Stephen F Traynelis
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA, 30322, USA.
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Emory Neurodegenerative Disease Center, Atlanta, GA, 30322, USA.
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4
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Santos-Gómez A, García-Recio A, Miguez-Cabello F, Soto D, Altafaj X, Olivella M. Identification of homologous GluN subunits variants accelerates GRIN variants stratification. Front Cell Neurosci 2022; 16:998719. [PMID: 36619673 PMCID: PMC9816381 DOI: 10.3389/fncel.2022.998719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
The clinical spectrum of GRIN-related neurodevelopmental disorders (GRD) results from gene- and variant-dependent primary alterations of the NMDA receptor, disturbing glutamatergic neurotransmission. Despite GRIN gene variants' functional annotations being dually critical for stratification and precision medicine design, genetically diagnosed pathogenic GRIN variants currently outnumber their relative functional annotations. Based on high-resolution crystal 3D models and topological domains conservation between GluN1, GluN2A, and GluN2B subunits of the NMDAR, we have generated GluN1-GluN2A-GluN2B subunits structural superimposition model to find equivalent positions between GluN subunits. We have developed a GRIN structural algorithm that predicts functional changes in the equivalent structural positions in other GluN subunits. GRIN structural algorithm was computationally evaluated to the full GRIN missense variants repertoire, consisting of 4,525 variants. The analysis of this structure-based model revealed an absolute predictive power for GluN1, GluN2A, and GluN2B subunits, both in terms of pathogenicity-association (benign vs. pathogenic variants) and functional impact (loss-of-function, benign, gain-of-function). Further, we validated this computational algorithm experimentally, using an in silico library of GluN2B-equivalent GluN2A artificial variants, designed from pathogenic GluN2B variants. Thus, the implementation of the GRIN structural algorithm allows to computationally predict the pathogenicity and functional annotations of GRIN variants, resulting in the duplication of pathogenic GRIN variants assignment, reduction by 30% of GRIN variants with uncertain significance, and increase by 70% of functionally annotated GRIN variants. Finally, GRIN structural algorithm has been implemented into GRIN variants Database (http://lmc.uab.es/grindb), providing a computational tool that accelerates GRIN missense variants stratification, contributing to clinical therapeutic decisions for this neurodevelopmental disorder.
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Affiliation(s)
- Ana Santos-Gómez
- Neurophysiology Laboratory, Department of Biomedicine, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Adrián García-Recio
- Bioinfomatics and Medical Statistics Group, University of Vic—Central University of Catalonia, Barcelona, Spain
| | - Federico Miguez-Cabello
- Neurophysiology Laboratory, Department of Biomedicine, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - David Soto
- Neurophysiology Laboratory, Department of Biomedicine, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Xavier Altafaj
- Neurophysiology Laboratory, Department of Biomedicine, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain,*Correspondence: Xavier Altafaj Mireia Olivella
| | - Mireia Olivella
- Bioinfomatics and Medical Statistics Group, University of Vic—Central University of Catalonia, Barcelona, Spain,*Correspondence: Xavier Altafaj Mireia Olivella
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5
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Benke TA, Park K, Krey I, Camp CR, Song R, Ramsey AJ, Yuan H, Traynelis SF, Lemke J. Clinical and therapeutic significance of genetic variation in the GRIN gene family encoding NMDARs. Neuropharmacology 2021; 199:108805. [PMID: 34560056 PMCID: PMC8525401 DOI: 10.1016/j.neuropharm.2021.108805] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 07/21/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 02/03/2023]
Abstract
Considerable genetic variation of N-methyl-d-aspartate receptors (NMDARs) has recently become apparent, with many hundreds of de novo variants identified through widely available clinical genetic testing. Individuals with GRIN variants present with neurological conditions such as epilepsy, autism, intellectual disability (ID), movement disorders, schizophrenia and behavioral disorders. Determination of the functional consequence of genetic variation for NMDARs should lead to precision therapeutics. Furthermore, genetic animal models harboring human variants have the potential to reveal mechanisms that are shared among different neurological conditions, providing strategies that may allow treatment of individuals who are refractory to therapy. Preclinical studies in animal models and small open label trials in humans support this idea. However, additional functional data for variants and animal models corresponding to multiple individuals with the same genotype are needed to validate this approach and to lead to thoughtfully designed, randomized, placebo-controlled clinical trials, which could provide data in order to determine safety and efficacy of potential precision therapeutics.
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Affiliation(s)
- Tim A Benke
- Departments of Pediatrics, Pharmacology, Neurology, and Otolaryngology, University of Colorado, School of Medicine and Children's Hospital Colorado, United States.
| | - Kristen Park
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine and Children's Hospital Colorado, United States
| | - Ilona Krey
- Institute of Human Genetics, Leipzig Medical Center, Leipzig, Germany
| | - Chad R Camp
- Department of Pharmacology and Chemical Biology and the Center for Functional Evaluation of Rare Variants, Emory University School of Medicine, Atlanta, GA, United States
| | - Rui Song
- Department of Pharmacology and Chemical Biology and the Center for Functional Evaluation of Rare Variants, Emory University School of Medicine, Atlanta, GA, United States
| | - Amy J Ramsey
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada
| | - Hongjie Yuan
- Department of Pharmacology and Chemical Biology and the Center for Functional Evaluation of Rare Variants, Emory University School of Medicine, Atlanta, GA, United States
| | - Stephen F Traynelis
- Department of Pharmacology and Chemical Biology and the Center for Functional Evaluation of Rare Variants, Emory University School of Medicine, Atlanta, GA, United States
| | - Johannes Lemke
- Institute of Human Genetics, Leipzig Medical Center, Leipzig, Germany
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6
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Kellner S, Abbasi A, Carmi I, Heinrich R, Garin-Shkolnik T, Hershkovitz T, Giladi M, Haitin Y, Johannesen KM, Steensbjerre Møller R, Berlin S. Two de novo GluN2B mutations affect multiple NMDAR-functions and instigate severe pediatric encephalopathy. eLife 2021; 10:67555. [PMID: 34212862 PMCID: PMC8260228 DOI: 10.7554/elife.67555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 02/15/2021] [Accepted: 06/27/2021] [Indexed: 12/15/2022] Open
Abstract
The N-methyl-D-aspartate receptors (NMDARs; GluNRS) are glutamate receptors, commonly located at excitatory synapses. Mutations affecting receptor function often lead to devastating neurodevelopmental disorders. We have identified two toddlers with different heterozygous missense mutations of the same, and highly conserved, glycine residue located in the ligand-binding-domain of GRIN2B: G689C and G689S. Structure simulations suggest severely impaired glutamate binding, which we confirm by functional analysis. Both variants show three orders of magnitude reductions in glutamate EC50, with G689S exhibiting the largest reductions observed for GRIN2B (~2000-fold). Moreover, variants multimerize with, and upregulate, GluN2Bwt-subunits, thus engendering a strong dominant-negative effect on mixed channels. In neurons, overexpression of the variants instigates suppression of synaptic GluNRs. Lastly, while exploring spermine potentiation as a potential treatment, we discovered that the variants fail to respond due to G689’s novel role in proton-sensing. Together, we describe two unique variants with extreme effects on channel function. We employ protein-stability measures to explain why current (and future) LBD mutations in GluN2B primarily instigate Loss-of-Function.
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Affiliation(s)
- Shai Kellner
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Abeer Abbasi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ido Carmi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ronit Heinrich
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | | | | | - Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katrine M Johannesen
- Department of Epilepsy Genetics and Personalized Treatment, the Danish Epilepsy Centre, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Rikke Steensbjerre Møller
- Department of Epilepsy Genetics and Personalized Treatment, the Danish Epilepsy Centre, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Shai Berlin
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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7
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Chitnaduku Thippeswamy M, Kuchibhatla SAR, Rajagopal P. Concentric shell gradient index metamaterials for focusing ultrasound in bulk media. Ultrasonics 2021; 114:106424. [PMID: 33819870 DOI: 10.1016/j.ultras.2021.106424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Focusing of ultrasound waves is criticalto a number ofclinical andindustrial applications including biomedical and underwater imaging,nondestructive evaluation and material processing. This paper discusses the use of a novel'add-on' gradient refractive index (GRIN) metamaterial structure made ofconcentric shells,to focus ultrasonic waves generated by conventional transducers. Analysis based on the Huygen's principle and numerical simulations is used to design the geometric and material properties of the proposed structure, whose working is demonstrated through experiments. Varying the shell material or thickness is shown to offer an elegant and straightforward way to tailor the focal spot inside the target material. The concentric-shell GRIN lens proposed here has a simple design, and has a potential to be used in dynamic focusing without advanced lenses or electronic steering.
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Affiliation(s)
- Manjunath Chitnaduku Thippeswamy
- Centre for Nondestructive Evaluation, Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India
| | - Sai Aditya Raman Kuchibhatla
- Centre for Nondestructive Evaluation, Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India
| | - Prabhu Rajagopal
- Centre for Nondestructive Evaluation, Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India.
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8
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Nudmamud-Thanoi S, Iamjan SA, Kerdsan-Phusan W, Thanoi S. Pharmacogenetics of drug dependence: Polymorphisms of genes involved in glutamate neurotransmission. Neurosci Lett 2020; 726:134128. [PMID: 30836121 DOI: 10.1016/j.neulet.2019.02.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/09/2018] [Revised: 02/16/2019] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
Multiple studies provide evidence to support dysfunction of glutamate neurotransmission in the pathogenesis of drug dependence. Pharmacogenetic investigation of glutamate-related genes has provided further support for the involvement of this neurotransmitter in the risk of, and consequences of, drug abuse and dependence. This paper aims to provide a brief review of these association studies. Findings involving single nucleotide polymorphisms (SNPs) in glutamate receptor genes (GRIN, GRIA) and glutamate transporter genes (SLC1A, SLC17A) are reviewed as potential risk factors. As yet a clear perspective of the functional consequences and interactions of the various reported findings is lacking.
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Affiliation(s)
- Sutisa Nudmamud-Thanoi
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand.
| | - Sri-Arun Iamjan
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Walailuk Kerdsan-Phusan
- Department of Anatomy, School of Medical Sciences, University of Phayao, Phayao 56000, Thailand
| | - Samur Thanoi
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
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9
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Ziegler G, Nelson R, Granada S, Krishnan HB, Gillman JD, Baxter I. Genomewide association study of ionomic traits on diverse soybean populations from germplasm collections. Plant Direct 2018; 2:e00033. [PMID: 31245681 PMCID: PMC6508489 DOI: 10.1002/pld3.33] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/06/2017] [Accepted: 11/14/2017] [Indexed: 05/17/2023]
Abstract
The elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is chemically stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the efficacy of using samples from germplasm banks for gene discovery, we analyzed the elemental profile of seeds from 1,653 lines in the USDA Soybean Germplasm Collection. We observed large differences in the elemental profiles based on where the lines were grown, which lead us to break up the genetic analysis into multiple small experiments. Despite these challenges, we were able to identify candidate single nucleotide polymorphisms (SNPs) controlling elemental accumulation as well as lines with extreme elemental accumulation phenotypes. Our results suggest that elemental analysis of germplasm samples can identify SNPs in linkage disequilibrium to genes, which can be leveraged to assist in crop improvement efforts.
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Affiliation(s)
- Greg Ziegler
- USDA‐ARS Plant Genetics Research UnitSt. LouisMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Randall Nelson
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit and Department of Crop SciencesUSDA‐ARSUniversity of IllinoisUrbanaILUSA
| | | | - Hari B. Krishnan
- USDA‐ARS Plant Genetics Research UnitColumbiaMOUSA
- Plant Science DivisionUniversity of MissouriColumbiaMOUSA
| | - Jason D. Gillman
- USDA‐ARS Plant Genetics Research UnitColumbiaMOUSA
- Plant Science DivisionUniversity of MissouriColumbiaMOUSA
| | - Ivan Baxter
- USDA‐ARS Plant Genetics Research UnitSt. LouisMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
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10
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Abstract
A significant number of variants/mutations in the N-methyl-D-aspartate glutamatergic receptor (NMDAR) gene family (GRIN) have been identified along with stunning advances in the technologies of next generation of whole-exome sequencing. Mutations in human GRIN genes are distributed throughout the entire gene, from amino terminal domain to C-terminal domain, in patients with various neuropsychiatric disorders, including autism spectrum disorders, epilepsy, intellectual disability, attention deficit hyperactivity disorder, and schizophrenia. Analyzing the currently available human genetic variations illustrates the genetic variation intolerance to missense mutations differs significantly among domains within the GRIN genes. Functional analyses of these mutations and their pharmacological profiles provide the first opportunity to understand the molecular mechanism and targeted therapeutic strategies for these neurological and psychiatric disorders, as well as unfold novel clues to channel function.
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Affiliation(s)
- Wenshu XiangWei
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing 100034, China
| | - Yuwu Jiang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing 100034, China.,Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing 100069, China
| | - Hongjie Yuan
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA 30322, USA
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Bassnett S, Costello MJ. The cause and consequence of fiber cell compaction in the vertebrate lens. Exp Eye Res 2016; 156:50-57. [PMID: 26992780 DOI: 10.1016/j.exer.2016.03.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 11/13/2015] [Revised: 03/02/2016] [Accepted: 03/11/2016] [Indexed: 01/02/2023]
Abstract
Fiber cells of the ocular lens are arranged in a series of concentric shells. New growth shells are added continuously to the lens surface and, as a consequence, the preexisting shells are buried. To focus light, the refractive index of the lens cytoplasm must exceed that of the surrounding aqueous and vitreous humors, and to that end, lens cells synthesize high concentrations of soluble proteins, the crystallins. To correct for spherical aberration, it is necessary that the crystallin concentration varies from shell-to-shell, such that cellular protein content is greatest in the center of the lens. The radial variation in protein content underlies the critical gradient index (GRIN) structure of the lens. Only the outermost shells of lens fibers contain the cellular machinery necessary for protein synthesis. It is likely, therefore, that the GRIN (which spans the synthetically inactive, organelle-free zone of the lens) does not result from increased levels of protein synthesis in the core of the lens but is instead generated through loss of volume by inner fiber cells. Because volume is lost primarily in the form of cell water, the residual proteins in the central lens fibers can be concentrated to levels of >500 mg/ml. In this short review, we describe the process of fiber cell compaction, its relationship to lens growth and GRIN formation, and offer some thoughts on the likely nature of the underlying mechanism.
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Affiliation(s)
- Steven Bassnett
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, USA.
| | - M Joseph Costello
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, USA
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Howlett ID, Gordon M, Brownlee JW, Barton JK, Kostuk RK. Volume Holographic Reflection Endoscope for In-Vivo Ovarian Cancer Clinical Studies. Proc SPIE Int Soc Opt Eng 2014; 2014. [PMID: 25009709 DOI: 10.1117/12.2037859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present the design for an endoscopic system capable of imaging tissues of the ovary at two selected imaging depths simultaneously. The method utilizes a multiplexed volume hologram to select wavefronts from different depths within the tissue. It is the first demonstration of an endoscopic volume holographic imaging system. The endoscope uses both gradient index (GRIN) optical components and off the shelf singlet lenses to relay an image from the distal tip to the proximal end. The endoscope has a minimum diameter of 3.75 mm. The system length is 30 cm which is connected to a handle that includes the holographic components and optics that relay the image to a camera. Preliminary evaluation of the endoscope was performed with tissue phantoms and calibrated targets, which shows lateral resolution ≈ 4 μm at an operating wavelength of 660 nm. The hologram is recorded in phenanthraquinone doped poly methacrylate and is designed to produce images from two tissue depths. One image is obtained at the tissue surface and the second 70 μm below the surface. This method requires no mechanical scanning and acquires an image at the camera frame rate. The preliminary ex-vivo results show good correlation with histology sections of the same tissue sections.
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Affiliation(s)
- I D Howlett
- Photonic Systems Lab; Department of Electrical and Computer Engineering, University of Arizona, Tucson, AZ 85721 ; College of Optical Science, University of Arizona, Tucson, AZ 85721
| | - M Gordon
- Photonic Systems Lab; Department of Electrical and Computer Engineering, University of Arizona, Tucson, AZ 85721 ; College of Optical Science, University of Arizona, Tucson, AZ 85721
| | - J W Brownlee
- Photonic Systems Lab; Department of Electrical and Computer Engineering, University of Arizona, Tucson, AZ 85721 ; College of Optical Science, University of Arizona, Tucson, AZ 85721
| | - J K Barton
- College of Optical Science, University of Arizona, Tucson, AZ 85721 ; Biomedical Engineering, University of Arizona, Tucson, AZ 85721
| | - R K Kostuk
- Photonic Systems Lab; Department of Electrical and Computer Engineering, University of Arizona, Tucson, AZ 85721 ; College of Optical Science, University of Arizona, Tucson, AZ 85721
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Abstract
Amino acids in wheat (Triticum aestivum) seeds mainly accumulate in storage proteins called gliadins and glutenins. Gliadins contain α/β-, γ- and ω-types whereas glutenins contain HMW- and LMW-types. Known gliadin and glutenin sequences were largely determined through cloning and sequencing by capillary electrophoresis. This time-consuming process prevents us to intensively study the variation of each orthologous gene copy among cultivars. The throughput and sequencing length of Pacific Bioscience RS (PacBio) single molecule sequencing platform make it feasible to construct contiguous and non-chimeric RNA sequences. We assembled 424 wheat storage protein transcripts from ten wheat cultivars by using just one single-molecule-real-time cell. The protein genes from wheat cultivar Chinese Spring are comparable to known sequences from NCBI. We demonstrated real-time sequencing of gene families with high-throughput and low-cost. This method can be applied to studies of gene amplification and copy number variation among species and cultivars.
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Affiliation(s)
- Wei Zhang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
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de Castro A, Birkenfeld J, Maceo B, Manns F, Arrieta E, Parel JM, Marcos S. Influence of shape and gradient refractive index in the accommodative changes of spherical aberration in nonhuman primate crystalline lenses. Invest Ophthalmol Vis Sci 2013; 54:6197-207. [PMID: 23927893 PMCID: PMC3771709 DOI: 10.1167/iovs.13-11996] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [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: 03/08/2013] [Accepted: 07/17/2013] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To estimate changes in surface shape and gradient refractive index (GRIN) profile in primate lenses as a function of accommodation. To quantify the contribution of surface shape and GRIN to spherical aberration changes with accommodation. METHODS Crystalline lenses from 15 cynomolgus monkeys were studied in vitro under different levels of accommodation produced by a stretching system. Lens shape was obtained from optical coherence tomography (OCT) cross-sectional images. The GRIN was reconstructed with a search algorithm using the optical path measured from OCT images and the measured back focal length. The spherical aberration of the lens was estimated as a function of accommodation using the reconstructed GRIN and a homogeneous refractive index. RESULTS The lens anterior and posterior radii of curvature decreased with increasing lens power. Both surfaces exhibited negative asphericities in the unaccommodated state. The anterior surface conic constant shifted toward less negative values with accommodation, while the value of the posterior remained constant. GRIN parameters remained constant with accommodation. The lens spherical aberration with GRIN distribution was negative and higher in magnitude than that with a homogeneous equivalent refractive index (by 29% and 53% in the unaccommodated and fully accommodated states, respectively). Spherical aberration with the equivalent refractive index shifted with accommodation toward negative values (-0.070 μm/diopter [D]), but the reconstructed GRIN shifted it farther (-0.124 μm/D). CONCLUSIONS When compared with the lens with the homogeneous equivalent refractive index, the reconstructed GRIN lens has more negative spherical aberration and a larger shift toward more negative values with accommodation.
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Affiliation(s)
- Alberto de Castro
- Instituto de Óptica “Daza de Valdés,” Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Judith Birkenfeld
- Instituto de Óptica “Daza de Valdés,” Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Bianca Maceo
- Ophthalmic and Biophysics Center, Bascom Palmer Eye Institute, University of Miami, Miller School of Medicine, Miami, Florida
- Biomedical Optics Laboratory, Department of Biomedical Engineering, University of Miami College of Engineering, Coral Gables, Florida
| | - Fabrice Manns
- Ophthalmic and Biophysics Center, Bascom Palmer Eye Institute, University of Miami, Miller School of Medicine, Miami, Florida
- Biomedical Optics Laboratory, Department of Biomedical Engineering, University of Miami College of Engineering, Coral Gables, Florida
| | - Esdras Arrieta
- Ophthalmic and Biophysics Center, Bascom Palmer Eye Institute, University of Miami, Miller School of Medicine, Miami, Florida
| | - Jean-Marie Parel
- Ophthalmic and Biophysics Center, Bascom Palmer Eye Institute, University of Miami, Miller School of Medicine, Miami, Florida
| | - Susana Marcos
- Instituto de Óptica “Daza de Valdés,” Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Abstract
It is humbling to think that 30 years have passed since the paper by Collingridge, Kehl and McLennan showing that one of Jeff Watkins most interesting compounds, R-2-amino-5-phosphonopentanoate (d-AP5), blocked the induction of long-term potentiation in vitro at synapses from area CA3 of the hippocampus to CA1 without apparent effect on baseline synaptic transmission (Collingridge et al., 1983). This dissociation was one of the key triggers for an explosion of interest in glutamate receptors, and much has been discovered since that collectively contributes to our contemporary understanding of glutamatergic synapses - their biophysics and subunit composition, of the agonists and antagonists acting on them, and their diverse functions in different networks of the brain and spinal cord. It can be fairly said that Collingridge et al.'s (1983) observation was the stimulus that has led, on the one hand, to structural biological work at the atomic scale describing the key features of NMDA receptors that enables their coincidence function to happen; and, on the other, to work with whole animals investigating the contributions that calcium signalling via this receptor can have on rhythmical activities controlled by spinal circuits, memory encoding in the hippocampus (the topic of this article), visual cortical plasticity, sensitization in pain, and other functions. In this article, I lay out how my then interest in long-term potentiation (LTP) as a model of memory enabled me to recognise the importance of Collingridge et al.'s discovery - and how I and my colleagues endeavoured to take things forward in the area of learning and memory. This is in some respects a personal story, and I tell it as such. The idea that NMDA receptor activation is essential for memory encoding, though not for storage, took time to develop and to be accepted. Along the way, there have been confusions, challenges, and surprises surrounding the idea that activation of NMDA receptors can trigger memory. Some of these are described and how they have been addressed and resolved. Last, I touch on some new directions of interest with respect to the functional role of the NMDA receptor in cognition. This article is part of the Special Issue entitled 'Glutamate Receptor-Dependent Synaptic Plasticity'.
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Affiliation(s)
- Richard G M Morris
- Centre for Cognitive and Neural Systems, Edinburgh Neuroscience, The University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ, UK.
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