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Kumar S, Dasgupta S, Sajadi MM, Snyder GA, DeVico AL, Ray K. Discordant Antigenic Properties of Soluble and Virion SARS-CoV-2 Spike Proteins. Viruses 2024; 16:407. [PMID: 38543772 PMCID: PMC10974403 DOI: 10.3390/v16030407] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 04/01/2024] Open
Abstract
Efforts to develop vaccine and immunotherapeutic countermeasures against the COVID-19 pandemic focus on targeting the trimeric spike (S) proteins of SARS-CoV-2. Vaccines and therapeutic design strategies must impart the characteristics of virion S from historical and emerging variants onto practical constructs such as soluble, stabilized trimers. The virus spike is a heterotrimer of two subunits: S1, which includes the receptor binding domain (RBD) that binds the cell surface receptor ACE2, and S2, which mediates membrane fusion. Previous studies suggest that the antigenic, structural, and functional characteristics of virion S may differ from current soluble surrogates. For example, it was reported that certain anti-glycan, HIV-1 neutralizing monoclonal antibodies bind soluble SARS-CoV-2 S but do not neutralize SARS-CoV-2 virions. In this study, we used single-molecule fluorescence correlation spectroscopy (FCS) under physiologically relevant conditions to examine the reactivity of broadly neutralizing and non-neutralizing anti-S human monoclonal antibodies (mAbs) isolated in 2020. Binding efficiency was assessed by FCS with soluble S trimers, pseudoviruses and inactivated wild-type virions representing variants emerging from 2020 to date. Anti-glycan mAbs were tested and compared. We find that both anti-S specific and anti-glycan mAbs exhibit variable but efficient binding to a range of stabilized, soluble trimers. Across mAbs, the efficiencies of soluble S binding were positively correlated with reactivity against inactivated virions but not pseudoviruses. Binding efficiencies with pseudoviruses were generally lower than with soluble S or inactivated virions. Among neutralizing mAbs, potency did not correlate with binding efficiencies on any target. No neutralizing activity was detected with anti-glycan antibodies. Notably, the virion S released from membranes by detergent treatment gained more efficient reactivity with anti-glycan, HIV-neutralizing antibodies but lost reactivity with all anti-S mAbs. Collectively, the FCS binding data suggest that virion surfaces present appreciable amounts of both functional and nonfunctional trimers, with neutralizing anti-S favoring the former structures and non-neutralizing anti-glycan mAbs binding the latter. S released from solubilized virions represents a nonfunctional structure bound by anti-glycan mAbs, while engineered soluble trimers present a composite structure that is broadly reactive with both mAb types. The detection of disparate antigenicity and immunoreactivity profiles in engineered and virion-associated S highlight the value of single-virus analyses in designing future antiviral strategies against SARS-CoV-2.
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Affiliation(s)
- Sameer Kumar
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Mohammad M. Sajadi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Division of Clinical Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Greg A. Snyder
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Anthony L. DeVico
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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2
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Dasgupta S, Thomas JA, Ray K. Mechanism of Viral DNA Packaging in Phage T4 Using Single-Molecule Fluorescence Approaches. Viruses 2024; 16:192. [PMID: 38399968 PMCID: PMC10893049 DOI: 10.3390/v16020192] [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: 12/29/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the mechanisms responsible for DNA translocation. Over the last fifteen years, single-molecule fluorescence technologies have been applied to study viral nucleic acid packaging using the robust and flexible T4 in vitro packaging system in conjunction with genetic, biochemical, and structural analyses. In this review, we discuss the novel findings from these studies, including that the T4 genome was determined to be packaged as an elongated loop via the colocalization of dye-labeled DNA termini above the portal structure. Packaging efficiency of the TerL motor was shown to be inherently linked to substrate structure, with packaging stalling at DNA branches. The latter led to the design of multiple experiments whose results all support a proposed torsional compression translocation model to explain substrate packaging. Evidence of substrate compression was derived from FRET and/or smFRET measurements of stalled versus resolvase released dye-labeled Y-DNAs and other dye-labeled substrates relative to motor components. Additionally, active in vivo T4 TerS fluorescent fusion proteins facilitated the application of advanced super-resolution optical microscopy toward the visualization of the initiation of packaging. The formation of twin TerS ring complexes, each expected to be ~15 nm in diameter, supports a double protein ring-DNA synapsis model for the control of packaging initiation, a model that may help explain the variety of ring structures reported among pac site phages. The examination of the dynamics of the T4 packaging motor at the single-molecule level in these studies demonstrates the value of state-of-the-art fluorescent tools for future studies of complex viral replication mechanisms.
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Affiliation(s)
- Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Julie A. Thomas
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA;
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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Klontz E, Obi JO, Wang Y, Glendening G, Carr J, Tsibouris C, Buddula S, Nallar S, Soares AS, Beckett D, Redzic JS, Eisenmesser E, Palm C, Schmidt K, Scudder AH, Obiorah T, Essuman K, Milbrandt J, Diantonio A, Ray K, Snyder MLD, Deredge D, Snyder GA. The structure of NAD + consuming protein Acinetobacter baumannii TIR domain shows unique kinetics and conformations. J Biol Chem 2023; 299:105290. [PMID: 37758001 PMCID: PMC10641520 DOI: 10.1016/j.jbc.2023.105290] [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: 05/25/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Toll-like and interleukin-1/18 receptor/resistance (TIR) domain-containing proteins function as important signaling and immune regulatory molecules. TIR domain-containing proteins identified in eukaryotic and prokaryotic species also exhibit NAD+ hydrolase activity in select bacteria, plants, and mammalian cells. We report the crystal structure of the Acinetobacter baumannii TIR domain protein (AbTir-TIR) with confirmed NAD+ hydrolysis and map the conformational effects of its interaction with NAD+ using hydrogen-deuterium exchange-mass spectrometry. NAD+ results in mild decreases in deuterium uptake at the dimeric interface. In addition, AbTir-TIR exhibits EX1 kinetics indicative of large cooperative conformational changes, which are slowed down upon substrate binding. Additionally, we have developed label-free imaging using the minimally invasive spectroscopic method 2-photon excitation with fluorescence lifetime imaging, which shows differences in bacteria expressing native and mutant NAD+ hydrolase-inactivated AbTir-TIRE208A protein. Our observations are consistent with substrate-induced conformational changes reported in other TIR model systems with NAD+ hydrolase activity. These studies provide further insight into bacterial TIR protein mechanisms and their varying roles in biology.
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Affiliation(s)
- Erik Klontz
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Juliet O Obi
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Yajing Wang
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA; Department of Physiology, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Gabrielle Glendening
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Jahid Carr
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Constantine Tsibouris
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Sahthi Buddula
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Shreeram Nallar
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA; Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Alexei S Soares
- Brookhaven National Laboratory, National Synchrotron Light Source II, Structural Biology Program, Upton, New York, USA
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado, USA
| | - Elan Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado, USA
| | - Cheyenne Palm
- Department of Biological Sciences, Towson University, Towson, Maryland, USA
| | - Katrina Schmidt
- Department of Biological Sciences, Towson University, Towson, Maryland, USA
| | - Alexis H Scudder
- Department of Biological Sciences, Towson University, Towson, Maryland, USA
| | - Trinity Obiorah
- Department of Biological Sciences, Towson University, Towson, Maryland, USA
| | - Kow Essuman
- Department of Developmental Biology, Washington University School of Medicine, St Louis, Missouri, USA; Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jeffrey Milbrandt
- Department of Developmental Biology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Aaron Diantonio
- Department of Developmental Biology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA; Department of Biochemistry and Molecular Biology at the University of Maryland, School of Medicine, Baltimore, Maryland, USA
| | | | - Daniel Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Greg A Snyder
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA; Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA.
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Snyder GA, Kumar S, Lewis GK, Ray K. Two-photon fluorescence lifetime imaging microscopy of NADH metabolism in HIV-1 infected cells and tissues. Front Immunol 2023; 14:1213180. [PMID: 37662898 PMCID: PMC10468605 DOI: 10.3389/fimmu.2023.1213180] [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: 04/27/2023] [Accepted: 07/21/2023] [Indexed: 09/05/2023] Open
Abstract
Rapid detection of microbial-induced cellular changes during the course of an infection is critical to understanding pathogenesis and immunological homeostasis. In the last two decades, fluorescence imaging has received significant attention for its ability to help characterize microbial induced cellular and tissue changes in in vitro and in vivo settings. However, most of these methods rely on the covalent conjugation of large exogenous probes and detection methods based on intensity-based imaging. Here, we report a quantitative, intrinsic, label-free, and minimally invasive method based on two-photon fluorescence lifetime (FLT) imaging microscopy (2p-FLIM) for imaging 1,4-dihydro-nicotinamide adenine dinucleotide (NADH) metabolism of virally infected cells and tissue sections. To better understand virally induced cellular and tissue changes in metabolism we have used 2p-FLIM to study differences in NADH intensity and fluorescence lifetimes in HIV-1 infected cells and tissues. Differences in NADH fluorescence lifetimes are associated with cellular changes in metabolism and changes in cellular metabolism are associated with HIV-1 infection. NADH is a critical co-enzyme and redox regulator and an essential biomarker in the metabolic processes. Label-free 2p-FLIM application and detection of NADH fluorescence using viral infection systems are in their infancy. In this study, the application of the 2p-FLIM assay and quantitative analyses of HIV-1 infected cells and tissue sections reveal increased fluorescence lifetime and higher enzyme-bound NADH fraction suggesting oxidative phosphorylation (OxPhos) compared to uninfected cells and tissues. 2p-FLIM measurements improve signal to background, fluorescence specificity, provide spatial and temporal resolution of intracellular structures, and thus, are suitable for quantitative studies of cellular functions and tissue morphology. Furthermore, 2p-FLIM allows distinguishing free and bound populations of NADH by their different fluorescence lifetimes within single infected cells. Accordingly, NADH fluorescence measurements of individual single cells should provide necessary insight into the heterogeneity of metabolic activity of infected cells. Implementing 2p-FLIM to viral infection systems measuring NADH fluorescence at the single or subcellular level within a tissue can provide visual evidence, localization, and information in a real-time diagnostic or therapeutic metabolic workflow.
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Affiliation(s)
- Greg A. Snyder
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Sameer Kumar
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - George K. Lewis
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States
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5
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Hegde KR, Ray K, Szmacinski H, Sorto S, Puche AC, Lengyel I, Thompson RB. Two-Photon Excited Fluorescence Lifetime Imaging of Tetracycline-Labeled Retinal Calcification. Sensors (Basel) 2023; 23:6626. [PMID: 37514920 PMCID: PMC10386431 DOI: 10.3390/s23146626] [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: 04/07/2023] [Revised: 06/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Deposition of calcium-containing minerals such as hydroxyapatite and whitlockite in the subretinal pigment epithelial (sub-RPE) space of the retina is linked to the development of and progression to the end-stage of age-related macular degeneration (AMD). AMD is the most common eye disease causing blindness amongst the elderly in developed countries; early diagnosis is desirable, particularly to begin treatment where available. Calcification in the sub-RPE space is also directly linked to other diseases such as Pseudoxanthoma elasticum (PXE). We found that these mineral deposits could be imaged by fluorescence using tetracycline antibiotics as specific stains. Binding of tetracyclines to the minerals was accompanied by increases in fluorescence intensity and fluorescence lifetime. The lifetimes for tetracyclines differed substantially from the known background lifetime of the existing natural retinal fluorophores, suggesting that calcification could be visualized by lifetime imaging. However, the excitation wavelengths used to excite these lifetime changes were generally shorter than those approved for retinal imaging. Here, we show that tetracycline-stained drusen in post mortem human retinas may be imaged by fluorescence lifetime contrast using multiphoton (infrared) excitation. For this pilot study, ten eyes from six anonymous deceased donors (3 female, 3 male, mean age 83.7 years, range 79-97 years) were obtained with informed consent from the Maryland State Anatomy Board with ethical oversight and approval by the Institutional Review Board.
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Affiliation(s)
- Kavita R Hegde
- Department of Natural Sciences, Coppin State University, Baltimore, MD 21216, USA
| | - Krishanu Ray
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Henryk Szmacinski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sharon Sorto
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Adam C Puche
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Imre Lengyel
- The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Richard B Thompson
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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6
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Sonasang S, Jamsai M, Jalil M, Pham N, Ray K, Angkawisittpan N, Yupapin P, Boonkirdram S, Palomino-Ovando MA, Toledo-Solano M, Misaghian K, Lugo J. Corrigendum to "Multiband rabi antenna using nest microstrip add-drop filter (NMADF) for relativistic sensing applications" [Heliyon 9(2) (February 2023) e13611]. Heliyon 2023; 9:e16846. [PMID: 37539238 PMCID: PMC10394897 DOI: 10.1016/j.heliyon.2023.e16846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 08/05/2023] Open
Abstract
[This corrects the article DOI: 10.1016/j.heliyon.2023.e13611.].
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Affiliation(s)
- Somchat Sonasang
- Electronic Technology, Faculty of Industrial Technology, Nakon Phanom University, Nakon Phanom, 48000, Thailand
| | - M. Jamsai
- Department of Electrical Engineering, Faculty of Industry and Technology, Rajamagala University of Technology Isan Sakon Nakhon Campus, Sakon Nakhon, 47160, Thailand
| | - M.A. Jalil
- Department of Physics, Universiti Teknologi Malaysia, 81310, Skuda, Johor, Malaysia
| | - N.T. Pham
- Institute for Computational Science, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - K. Ray
- Amity School of Applied Sciences, Amity University Rajasthan, Jaipur, India
- Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y AV. 18 sur, Col. San Manuel Ciudad Universitaria, Pueble Pue, 72570, Mexico
- Faubert Lab, Ecole d'optométrie, Université de Montréal, Montréal, QC, H3T1P1, Canada
| | - Niwat Angkawisittpan
- Research Unit for Computational Electromagnetics and Optical Systems, Faculty of Engineering, Mahasarakham University, Maha Sarakham, 44150, Thailand
| | - Preecha Yupapin
- Department of Electrical Technology, School of Industrial Technology, Sakonnakhon Technical College, Institute of Vocational Education Northeastern 2, Sakonnakhon, 47000, Thailand
| | - Sarawoot Boonkirdram
- Program of Electrical and Electronics, Faculty of Industrial Technology, Sakon Nakhon Rajabhat University, 680 Nittayo, Mueang, Sakon Nakhon, 47000, Thailand
| | - Martha Alicia Palomino-Ovando
- Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y AV. 18 sur, Col. San Manuel Ciudad Universitaria, Pueble Pue, 72570, Mexico
| | - Miller Toledo-Solano
- CONACYT-Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Pueble, Av. San Claudio y Av. 18 sur, Col. San Manuel Ciudad Universitaria, Puebla Pue, 72570, Mexico
| | - Khashayar Misaghian
- Faubert Lab, School of Optometry, Université de Montréal, Montréal, QC, H3T1P1, Canada
- Sage-Sentinel Smart Solutions, 1919-1, Tancha, Onna-son Kunigamigun, Okinawa, 904-0495, Japan
| | - J.E. Lugo
- Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y AV. 18 sur, Col. San Manuel Ciudad Universitaria, Pueble Pue, 72570, Mexico
- Faubert Lab, School of Optometry, Université de Montréal, Montréal, QC, H3T1P1, Canada
- Sage-Sentinel Smart Solutions, 1919-1, Tancha, Onna-son Kunigamigun, Okinawa, 904-0495, Japan
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7
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Liang L, Zheng P, Jia S, Ray K, Chen Y, Barman I. Plasmonic Nanodiamonds. Nano Lett 2023; 23:5746-5754. [PMID: 37289011 DOI: 10.1021/acs.nanolett.3c01514] [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] [Indexed: 06/09/2023]
Abstract
While nitrogen-vacancy (NV) centers in diamonds have emerged as promising solid-state quantum emitters for sensing applications, the tantalizing possibility of coupling them with photonic or broadband plasmonic nanostructures to create ultrasensitive biolabels has not been fully realized. Indeed, it remains technologically challenging to create free-standing hybrid diamond-based imaging nanoprobes with enhanced brightness and high temporal resolution. Herein, we leverage the bottom-up DNA self-assembly to develop hybrid free-standing plasmonic nanodiamonds, which feature a closed plasmonic nanocavity completely encapsulating a single nanodiamond. Correlated single nanoparticle spectroscopical characterizations suggest that the plasmonic nanodiamond displays dramatically and simultaneously enhanced brightness and emission rate. We believe that they hold huge potential to serve as a stable solid-state single-photon source and could serve as a versatile platform to study nontrivial quantum effects in biological systems with enhanced spatial and temporal resolution.
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Affiliation(s)
- Le Liang
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
- Department of Ophthalmology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Peng Zheng
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sisi Jia
- Zhangjiang Lab, Shanghai 201210, China
| | - Krishanu Ray
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Yun Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
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8
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Liang L, Wu L, Zheng P, Ding T, Ray K, Barman I. DNA-Patched Nanoparticles for the Self-Assembly of Colloidal Metamaterials. JACS Au 2023; 3:1176-1184. [PMID: 37124309 PMCID: PMC10131209 DOI: 10.1021/jacsau.3c00013] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
Colloidal metamaterials are highly desired artificial materials that recapitulate the structure of simple molecules. They exhibit exceptional functionalities conferred by the organization of and specific interaction among constituent elements. Harvesting such exquisite attributes for potential applications necessitates establishing precise control over their structural configuration with high precision. Yet, creating molecule-like small clusters of colloidal metamaterials remains profoundly challenging, as a lack of regioselectively encoded surface chemical heterogeneity prevents specific recognition interactions. Herein, we report a new strategy by harnessing magnetic-bead-assisted DNA cluster transferring to create discretely DNA cluster-patched nanoparticles for the self-assembly of colloidal metamaterials. This strategy affords broad generalizability and scalability for robustly patching DNA clusters on nanoparticles unconstrained by geometrical, dimensional, and compositional complexities commonly encountered in colloidal materials at the nano- and microscale. We direct judiciously patched nanoparticles into a wide variety of nanoassemblies and present a case study demonstrating the distinct metamaterial properties in enhancing the spontaneous emission of diamond nanoparticles. This newly invented strategy is readily implementable and extendable to construct a palette of structurally sophisticated and functionality-explicit architecture, paving the way for nanoscale manipulation of colloidal material functionalities with wide-ranging applications for biological sensing, optical engineering, and catalytic chemistry.
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Affiliation(s)
- Le Liang
- The
Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
- Department
of Mechanical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Lintong Wu
- Department
of Mechanical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Peng Zheng
- Department
of Mechanical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Tao Ding
- The
Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Krishanu Ray
- Division
of Vaccine Research, Institute of Human Virology, Department of Biochemistry
and Molecular Biology, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - Ishan Barman
- Department
of Mechanical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Department
of Oncology, Johns Hopkins University School
of Medicine, Baltimore, Maryland 21287, United States
- Department
of Radiology & Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
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9
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Hegde KR, Puche AC, Szmacinski H, Fuller K, Ray K, Patel N, Lengyel I, Thompson RB. Fluorescence Lifetime Imaging of Human Sub-RPE Calcification In Vitro Following Chlortetracycline Infusion. Int J Mol Sci 2023; 24:6421. [PMID: 37047392 PMCID: PMC10094693 DOI: 10.3390/ijms24076421] [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: 01/05/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
We have shown that all sub-retinal pigment epithelial (sub-RPE) deposits examined contain calcium phosphate minerals: hydroxyapatite (HAP), whitlockite (Wht), or both. These typically take the form of ca. 1 μm diameter spherules or >10 μm nodules and appear to be involved in the development and progression of age-related macular degeneration (AMD). Thus, these minerals may serve as useful biomarkers the for early detection and monitoring of sub-RPE changes in AMD. We demonstrated that HAP deposits could be imaged in vitro by fluorescence lifetime imaging microscopy (FLIM) in flat-mounted retinas using legacy tetracycline antibiotics as selective sensors for HAP. As the contrast on a FLIM image is based on the difference in fluorescence lifetime and not intensity of the tetracycline-stained HAP, distinguishing tissue autofluorescence from the background is significantly improved. The focus of the present pilot study was to assess whether vascular perfusion of the well tolerated and characterized chlortetracycline (widely used as an orally bioavailable antibiotic) can fluorescently label retinal HAP using human cadavers. We found that the tetracycline delivered through the peripheral circulation can indeed selectively label sub-RPE deposits opening the possibility for its use for ophthalmic monitoring of a range of diseases in which deposit formation is reported, such as AMD and Alzheimer disease (AD).
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Affiliation(s)
- Kavita R. Hegde
- Department of Natural Sciences, Coppin State University, Baltimore, MD 21216, USA
| | - Adam C. Puche
- Department of Anatomy and Neurobiology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Henryk Szmacinski
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Kristina Fuller
- Department of Anatomy and Neurobiology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Krishanu Ray
- Institute for Human Virology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Nikita Patel
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
- Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
| | - Imre Lengyel
- The Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Richard B. Thompson
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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10
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Zheng P, Liang L, Arora S, Ray K, Semancik S, Barman I. Pyramidal hyperbolic metasurfaces enhance spontaneous emission of nitrogen-vacancy centers in nanodiamond. Adv Opt Mater 2023; 11:2202548. [PMID: 37920689 PMCID: PMC10619965 DOI: 10.1002/adom.202202548] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 11/04/2023]
Abstract
Nitrogen-vacancy (NV) centers in nanodiamond hold great promise for creating superior biological labels and quantum sensing methods. Yet, inefficient photon generation and extraction from excited NV centers restricts the achievable sensitivity and temporal resolution. Herein, we report an entirely complementary route featuring pyramidal hyperbolic metasurface to modify the spontaneous emission of NV centers. Fabricated using nanosphere lithography, the metasurface consists of alternatively stacked silica-silver thin films configured in a pyramidal fashion, and supports both spectrally broadband Purcell enhancement and spatially extended intense local fields owing to the hyperbolic dispersion and plasmonic coupling. The enhanced photophysical properties are manifested as a simultaneous amplification to the spontaneous decay rate and emission intensity of NV centers. We envision the reported pyramidal metasurface could serve as a versatile platform for creating chip-based ultrafast single-photon sources and spin-enhanced quantum biosensing strategies, as well as aiding in further fundamental understanding of photoexcited species in condensed phases.
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Affiliation(s)
- Peng Zheng
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
- Biomolecular Measurement Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Le Liang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
- The Institute of Advanced Studies, Wuhan University, China, 430072
| | - Saransh Arora
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Krishanu Ray
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, United States
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Steve Semancik
- Biomolecular Measurement Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
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11
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Merino VF, Yan Y, Ordonez AA, Bullen CK, Lee A, Saeki H, Ray K, Huang T, Jain SK, Pomper MG. Nucleolin mediates SARS-CoV-2 replication and viral-induced apoptosis of host cells. Antiviral Res 2023; 211:105550. [PMID: 36740097 PMCID: PMC9896859 DOI: 10.1016/j.antiviral.2023.105550] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 08/16/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
Host-oriented antiviral therapeutics are promising treatment options to combat COVID-19 and its emerging variants. However, relatively little is known about the cellular proteins hijacked by SARS-CoV-2 for its replication. Here we show that SARS-CoV-2 induces expression and cytoplasmic translocation of the nucleolar protein, nucleolin (NCL). NCL interacts with SARS-CoV-2 viral proteins and co-localizes with N-protein in the nucleolus and in stress granules. Knockdown of NCL decreases the stress granule component G3BP1, viral replication and improved survival of infected host cells. NCL mediates viral-induced apoptosis and stress response via p53. SARS-CoV-2 increases NCL expression and nucleolar size and number in lungs of infected hamsters. Inhibition of NCL with the aptamer AS-1411 decreases viral replication and apoptosis of infected cells. These results suggest nucleolin as a suitable target for anti-COVID therapies.
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Affiliation(s)
- Vanessa F Merino
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Yu Yan
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Alvaro A Ordonez
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - C Korin Bullen
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Albert Lee
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harumi Saeki
- Department of Human Pathology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Krishanu Ray
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sanjay K Jain
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martin G Pomper
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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12
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Sonasang S, Jamsai M, Jalil MA, Pham NT, Ray K, Angkawisittpan N, Yupapin P, Boonkirdram S, Palomino-Ovando MA, Toledo-Solano M, Misaghian K, Lugo JE. Multiband Rabi antenna using nest microstrip add-drop filter (NMADF) for relativistic sensing applications. Heliyon 2023; 9:e13611. [PMID: 36879752 PMCID: PMC9984424 DOI: 10.1016/j.heliyon.2023.e13611] [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: 10/20/2022] [Revised: 12/26/2022] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
A microstrip circuit is designed, constructed, and tested based on the nest microstrip add-drop filters (NMADF). The multi-level system oscillation is generated by the wave-particle behaviors of AC driven along the microstrip ring circular path. The continuous successive filtering is applied via the device input port. The higher-order harmonic oscillations can be filtered, from which the two-level system known as a Rabi oscillation is achieved. The outside microstrip ring energy is coupled to the inside rings, from which the multiband Rabi oscillations can be formed within the inner rings. The resonant Rabi frequencies can be applied for multi-sensing probes. The relationship between electron density and Rabi oscillation frequency of each microstrip ring output can be obtained and used for multi-sensing probe applications. The relativistic sensing probe can be obtained by the warp speed electron distribution at the resonant Rabi frequency respecting the resonant ring radii. These are available for relativistic sensing probe usage. The obtained experimental results have shown that there are 3-center Rabi frequencies obtained, which can be used for 3-sensing probes simultaneously. The sensing probe speeds of 1.1c, 1.4c, and 1.5c are obtained using the microstrip ring radii of 14.20, 20.12, and 34.49 mm, respectively. The best sensor sensitivity of 1.30 ms is achieved. The relativistic sensing platform can be used for many applications.
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Affiliation(s)
- Somchat Sonasang
- Electronics Technology, Faculty of Industrial Technology, Nakon Phanom University, Nakon Phanom 48000, Thailand
| | - M Jamsai
- Department of Electrical Engineering, Faculty of Industry and Technology, Rajamagala University of Technology Isan Sakon Nakhon Campus, Sakon Nakhon 47160, Thailand
| | - M A Jalil
- Department of Physics, Universiti Teknologi Malaysia, 81310 Skuda, Johor, Malaysia
| | - Nhat Truong Pham
- Institute for Computational Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - K Ray
- Amity School of Applied Sciences, Amity University Rajasthan, Jaipur, India.,Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y AV. 18 sur, Col. San Manuel Ciudad Universitaria, Pueble Pue 72570, Mexico.,Faubert Lab, School of Optometry, Université de Montréal, Montréal, QC H3T1P1, Canada
| | - Niwat Angkawisittpan
- Research Unit for Computational Electromagnetics and Optical Systems, Faculty of Engineering, Mahasarakham University, Maha Sarakham 44150, Thailand
| | - Preecha Yupapin
- Department of Electrical Technology, School of Industrial Technology, Sakonnakhon Technical College, Institute of Vocational Education Northeastern 2, Sakonnakhon 47000, Thailand
| | - Sarawoot Boonkirdram
- Program of Electrical and Electronics, Faculty of Industrial Technology, Sakon Nakhon Rajabhat University, 680 Nittayo, Mueang, Sakon Nakhon 47000, Thailand
| | - Martha Alicia Palomino-Ovando
- Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y AV. 18 sur, Col. San Manuel Ciudad Universitaria, Pueble Pue 72570, Mexico
| | - Miller Toledo-Solano
- CONACYT-Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Pueble, Av. San Claudio y Av. 18 sur, Col. San Manuel Ciudad Universitaria, Puebla Pue, 72570, Mexico
| | - Khashayar Misaghian
- Faubert Lab, School of Optometry, Université de Montréal, Montréal, QC H3T1P1, Canada.,Sage-Sentinel Smart Solutions, 1919-1 Tancha, Onna-son Kunigamigun, Okinawa, 904-0495, Japan
| | - J E Lugo
- Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y AV. 18 sur, Col. San Manuel Ciudad Universitaria, Pueble Pue 72570, Mexico.,Faubert Lab, School of Optometry, Université de Montréal, Montréal, QC H3T1P1, Canada.,Sage-Sentinel Smart Solutions, 1919-1 Tancha, Onna-son Kunigamigun, Okinawa, 904-0495, Japan
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13
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Maiya R, Dey S, Ray K, Menon GI. The interplay of active and passive mechanisms in slow axonal transport. Biophys J 2023; 122:333-345. [PMID: 36502274 PMCID: PMC9892612 DOI: 10.1016/j.bpj.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/24/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
A combination of intermittent active movement of transient aggregates and a paused state that intervenes between periods of active transport has been proposed to underlie the slow, directed transport of soluble proteins in axons. A component of passive diffusion in the axoplasm may also contribute to slow axonal transport, although quantitative estimates of the relative contributions of diffusive and active movement in the slow transport of a soluble protein, and in particular how they might vary across developmental stages, are lacking. Here, we propose and study a model for slow axonal transport, addressing data from bleach recovery measurements on a small, soluble, protein, choline acetyltransferase, in thin axons of the lateral chordotonal (lch5) sensory neurons of Drosophila. Choline acetyltransferase is mainly present in soluble form in the axon and catalyzes the acetylation of choline at the synapse. It does not form particulate structures in axons and moves at rates characteristic of slow component b (≈ 1-10 mm/day or 0.01-0.1 μm/s). Using our model, which incorporates active transport with paused and/or diffusive states, we predict bleach recovery, transport rates, and cargo trajectories obtained through kymographs, comparing these with experimental observations at different developmental stages. We show that changes in the diffusive fraction of cargo during these developmental stages dominate bleach recovery and that a combination of active motion with a paused state alone cannot reproduce the data. We compared predictions of the model with results from photoactivation experiments. The importance of the diffusive state in reproducing the bleach recovery signal in the slow axonal transport of small soluble proteins is our central result.
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Affiliation(s)
- Reshma Maiya
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India
| | - Swagata Dey
- National Brain Research Centre, NH-8, Manesar, Gurgaon, Haryana, India; Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India
| | - Krishanu Ray
- National Brain Research Centre, NH-8, Manesar, Gurgaon, Haryana, India; Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India.
| | - Gautam I Menon
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India; Department of Physics, Ashoka University, Sonepat, India; Department of Biology, Ashoka University, Sonepat, India.
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14
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Horspool AM, Sen-Kilic E, Malkowski AC, Breslow SL, Mateu-Borras M, Hudson MS, Nunley MA, Elliott S, Ray K, Snyder GA, Miller SJ, Kang J, Blackwood CB, Weaver KL, Witt WT, Huckaby AB, Pyles GM, Clark T, Al Qatarneh S, Lewis GK, Damron FH, Barbier M. Development of an anti- Pseudomonas aeruginosa therapeutic monoclonal antibody WVDC-5244. Front Cell Infect Microbiol 2023; 13:1117844. [PMID: 37124031 PMCID: PMC10140502 DOI: 10.3389/fcimb.2023.1117844] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/22/2023] [Indexed: 05/02/2023] Open
Abstract
The rise of antimicrobial-resistant bacterial infections is a crucial health concern in the 21st century. In particular, antibiotic-resistant Pseudomonas aeruginosa causes difficult-to-treat infections associated with high morbidity and mortality. Unfortunately, the number of effective therapeutic interventions against antimicrobial-resistant P. aeruginosa infections continues to decline. Therefore, discovery and development of alternative treatments are necessary. Here, we present pre-clinical efficacy studies on an anti-P. aeruginosa therapeutic monoclonal antibody. Using hybridoma technology, we generated a monoclonal antibody and characterized its binding to P. aeruginosa in vitro using ELISA and fluorescence correlation spectroscopy. We also characterized its function in vitro and in vivo against P. aeruginosa. The anti-P. aeruginosa antibody (WVDC-5244) bound P. aeruginosa clinical strains of various serotypes in vitro, even in the presence of alginate exopolysaccharide. In addition, WVDC-5244 induced opsonophagocytic killing of P. aeruginosa in vitro in J774.1 murine macrophage, and complement-mediated killing. In a mouse model of acute pneumonia, prophylactic administration of WVDC-5244 resulted in an improvement of clinical disease manifestations and reduction of P. aeruginosa burden in the respiratory tract compared to the control groups. This study provides promising pre-clinical efficacy data on a new monoclonal antibody with therapeutic potential for P. aeruginosa infections.
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Affiliation(s)
- Alexander M. Horspool
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Emel Sen-Kilic
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Aaron C. Malkowski
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Scott L. Breslow
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Margalida Mateu-Borras
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Matthew S. Hudson
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Mason A. Nunley
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Sean Elliott
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Krishanu Ray
- University of Maryland, Baltimore School of Medicine, Division of Vaccine Research, Institute of Human Virology, Baltimore, MD, United States
| | - Greg A. Snyder
- University of Maryland, Baltimore School of Medicine, Division of Vaccine Research, Institute of Human Virology, Baltimore, MD, United States
| | - Sarah Jo Miller
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Jason Kang
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Catherine B. Blackwood
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Kelly L. Weaver
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - William T. Witt
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Annalisa B. Huckaby
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Gage M. Pyles
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Tammy Clark
- Department of Pediatrics, Division of Cystic Fibrosis, West Virginia University, Morgantown, WV, United States
| | - Saif Al Qatarneh
- Department of Pediatrics, Division of Cystic Fibrosis, West Virginia University, Morgantown, WV, United States
| | - George K. Lewis
- University of Maryland, Baltimore School of Medicine, Division of Vaccine Research, Institute of Human Virology, Baltimore, MD, United States
| | - F. Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
- *Correspondence: Mariette Barbier,
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15
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Ghosh A, Khanam A, Ray K, Mathur P, Subramanian A, Poonia B, Kottilil S. CD38: an ecto-enzyme with functional diversity in T cells. Front Immunol 2023; 14:1146791. [PMID: 37180151 PMCID: PMC10172466 DOI: 10.3389/fimmu.2023.1146791] [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: 01/17/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023] Open
Abstract
CD38, a nicotinamide adenine dinucleotide (NAD)+ glycohydrolase, is considered an activation marker of T lymphocytes in humans that is highly expressed during certain chronic viral infections. T cells constitute a heterogeneous population; however, the expression and function of CD38 has been poorly defined in distinct T cell compartments. We investigated the expression and function of CD38 in naïve and effector T cell subsets in the peripheral blood mononuclear cells (PBMCs) from healthy donors and people with HIV (PWH) using flow cytometry. Further, we examined the impact of CD38 expression on intracellular NAD+ levels, mitochondrial function, and intracellular cytokine production in response to virus-specific peptide stimulation (HIV Group specific antigen; Gag). Naïve T cells from healthy donors showed remarkably higher levels of CD38 expression than those of effector cells with concomitant reduced intracellular NAD+ levels, decreased mitochondrial membrane potential and lower metabolic activity. Blockade of CD38 by a small molecule inhibitor, 78c, increased metabolic function, mitochondrial mass and mitochondrial membrane potential in the naïve T lymphocytes. PWH exhibited similar frequencies of CD38+ cells in the T cell subsets. However, CD38 expression increased on Gag-specific IFN-γ and TNF-α producing cell compartments among effector T cells. 78c treatment resulted in reduced cytokine production, indicating its distinct expression and functional profile in different T cell subsets. In summary, in naïve cells high CD38 expression reflects lower metabolic activity, while in effector cells it preferentially contributes to immunopathogenesis by increasing inflammatory cytokine production. Thus, CD38 may be considered as a therapeutic target in chronic viral infections to reduce ongoing immune activation.
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Affiliation(s)
- Alip Ghosh
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- *Correspondence: Alip Ghosh,
| | - Arshi Khanam
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Poonam Mathur
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Ananya Subramanian
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Bhawna Poonia
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shyam Kottilil
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
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16
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Ganguly S, Mukherjee N, Ray K, Mandal S, Dasgupta A, Mallath M, Chawla T, Ray M, Pipara A, Biswas B, Roy S, Ghosh J. 64P Clinical profile and treatment outcome of patients with non-metastatic colon cancer: A single institutional study from India. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.10.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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17
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Abstract
Kinesins, the microtubule-dependent mechanochemical enzymes, power a variety of intracellular movements. Regulation of Kinesin activity and Kinesin-Cargo interactions determine the direction, timing and flux of various intracellular transports. This review examines how phosphorylation of Kinesin subunits and adaptors influence the traffic driven by Kinesin-1, -2, and -3 family motors. Each family of Kinesins are phosphorylated by a partially overlapping set of serine/threonine kinases, and each event produces a unique outcome. For example, phosphorylation of the motor domain inhibits motility, and that of the stalk and tail domains induces cargo loading and unloading effects according to the residue and context. Also, the association of accessory subunits with cargo and adaptor proteins with the motor, respectively, is disrupted by phosphorylation. In some instances, phosphorylation by the same kinase on different Kinesins elicited opposite outcomes. We discuss how this diverse range of effects could manage the logistics of Kinesin-dependent, long-range intracellular transport.
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18
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Dutta P, Ray K. Ciliary membrane, localised lipid modification and cilia function. J Cell Physiol 2022; 237:2613-2631. [PMID: 35661356 DOI: 10.1002/jcp.30787] [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: 12/03/2021] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/08/2022]
Abstract
Cilium, a tiny microtubule-based cellular appendage critical for cell signalling and physiology, displays a large variety of receptors. The composition and turnover of ciliary lipids and receptors determine cell behaviour. Due to the exclusion of ribosomal machinery and limited membrane area, a cilium needs adaptive logistics to actively reconstitute the lipid and receptor compositions during development and differentiation. How is this dynamicity generated? Here, we examine whether, along with the Intraflagellar-Transport, targeted changes in sector-wise lipid composition could control the receptor localisation and functions in the cilia. We discuss how an interplay between ciliary lipid composition, localised lipid modification, and receptor function could contribute to cilia growth and signalling. We argue that lipid modification at the cell-cilium interface could generate an added thrust for a selective exchange of membrane lipids and the transmembrane and membrane-associated proteins.
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Affiliation(s)
- Priya Dutta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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19
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Kapoor T, Dubey P, Ray K. Time-lapse imaging of Drosophila testis for monitoring actin dynamics and sperm release. STAR Protoc 2022; 3:101020. [PMID: 34977674 PMCID: PMC8689351 DOI: 10.1016/j.xpro.2021.101020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Here we describe a simple step-by-step protocol for collecting high-resolution, time-lapse images of intact Drosophila testis ex vivo for a limited period using a confocal microscope, with minimum photo-toxic damage, to monitor spermatid individualization, coiling, and release. The F-actin dynamics during spermatid morphogenesis can be further investigated through laser ablations, Fluorescence-Recovery-After-Photobleaching, and drug treatments, using this protocol. For complete details on the use and execution of this protocol, please refer to Dubey et al. (2016), Dubey et al. (2019), and Kapoor et al. (2021). Protocol for time-lapse imaging of Drosophila testis ex vivo The protocol is useful for monitoring spermatid maturation and release Also, for high-resolution analysis of subcellular F-actin dynamics
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Affiliation(s)
- Tushna Kapoor
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
- Corresponding author
| | - Pankaj Dubey
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
- Corresponding author
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
- Corresponding author
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20
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Gadre P, Nitsure N, Mazumdar D, Gupta S, Ray K. The rates of stem cell division determine the cell cycle lengths of its lineage. iScience 2021; 24:103232. [PMID: 34746698 PMCID: PMC8555441 DOI: 10.1016/j.isci.2021.103232] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 09/10/2021] [Accepted: 10/01/2021] [Indexed: 01/10/2023] Open
Abstract
Adult stem cells and their transit-amplifying progeny alter their proliferation rates to maintain tissue homeostasis. To test how the division rates of stem cells and transit-amplifying progeny affect tissue growth and differentiation, we developed a computation strategy that estimates the average cell-cycle lengths (lifespans) of germline stem cells and their progeny from fixed-tissue demography in the Drosophila testis. Analysis of the wild-type data using this method indicated that during the germline transit-amplification, the cellular lifespans extend by nearly 1.3-fold after the first division and shrink by about 2-folds after the second division. Cell-autonomous perturbations of the stem cell lifespan accordingly altered the lifespans of successive transit-amplifying stages. Remarkably, almost 2-fold alterations in the lifespans of stem cells and their immediate daughters did not affect the subsequent differentiation. The results indicate that the early germline division rates can adjust the following division rates and the onset of differentiation. Prediction of cellular lifespan from the demography of transit-amplifying cells Lifespans of spermatogonial cells change anomalously during transit-amplification Anomalous lifespan extension during transit-amplification precedes the onset of Bam Lifespan changes of early TA stages readjust that of the subsequent stages
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Affiliation(s)
- Purna Gadre
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Nitin Nitsure
- School of Mathematics, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Debasmita Mazumdar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India.,Biology Department, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Samir Gupta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India.,Department of Molecular and Life Sciences, University Zurich, 80006 Zürich, Switzerland
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
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21
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Ray K, Bridges I, Bruckert E, Perrone-Filardi P, Annemans L, Sibartie M, Dhalwani N, Villa G. Potential cardiovascular risk reduction with evolocumab in the real world: a simulation in patients with a history of myocardial infarction from the HEYMANS register. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.2591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background/Introduction
FOURIER included 22,351 patients with a history of myocardial infarction (MI) and a median low-density lipoprotein cholesterol (LDL-C) of 2.4 mmol/L. Reducing LDL-C with evolocumab reduced the risk of major cardiovascular (CV) events by 1.3%, in absolute terms, over 2.2 years. Whether similar benefits might be observed in real-world evidence from evolocumab use is unknown.
Purpose
Simulate CV risk and assess the potential CV risk reduction among a large European cohort of evolocumab users with a history of MI.
Methods
We used interim data from HEYMANS, a register of patients initiating evolocumab in routine clinical practice across 12 European countries, from August 2015 with follow-up through July 2020. Demographic and clinical characteristics, lipid-lowering therapy (LLT), and lipid values were collected from routine medical records (6 months prior to evolocumab initiation through 30 months post initiation). Patients with a history of MI were considered and two sub-cohorts were created: recent MI (MI ≤1 year before evolocumab initiation) and remote MI (MI >1 year before evolocumab initiation). For each patient, we 1) simulated their CV risk using three different sources, correcting for age and LDL-C: i) the REACH equation, ii) FOURIER, iii) an observational study including FOURIER-like patients; 2) calculated their absolute LDL-C reduction on evolocumab; 3) simulated their relative risk reduction (RRR) by randomly sampling from the inverse probability distribution of the rate ratio per 1 mmol/L from the key secondary endpoint in the FOURIER landmark analysis; 4) calculated their absolute risk reduction (ARR) and number needed to treat (NNT) over 2 years (recent MI) or 10 years (remote MI).
Results
Our analysis included 90 recent MI and 489 remote MI patients initiating evolocumab in clinical practice per local reimbursement criteria, with up to 24 months follow-up. Median (inter-quartile range) age was 59 (53–67) and 61 (53–68) years in recent MI and remote MI patients, respectively. LDL-C before evolocumab was 3.8 (3.2–4.6) and 3.6 (3.0–4.5) mmol/L. Absolute LDL-C reduction on evolocumab was 2.2 (1.4–2.8) and 2.2 (1.6–2.8) mmol/L, meaning relative LDL-C reduction of 60% (44%-73%) and 62% (47%-72%), respectively. Predicted ARR with evolocumab was substantial, whether over 2 years (recent MI) or over 10 years (remote MI). See Table 1.
Conclusions
This cohort of evolocumab users in clinical practice had a higher baseline LDL-C and CV risk than patients enrolled in FOURIER. LDL-C reduction and RRR were very similar in recent MI and remote MI patients. However, patients with a recent MI had a higher short-term CV risk and therefore showed a larger ARR on evolocumab.
Funding Acknowledgement
Type of funding sources: Private company. Main funding source(s): Amgen
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Affiliation(s)
- K Ray
- Imperial College London, London, United Kingdom
| | - I Bridges
- Amgen Limited, Cambridge, United Kingdom
| | - E Bruckert
- University Pierre & Marie Curie Paris VI, Paris, France
| | | | | | - M Sibartie
- Amgen (Europe) GmbH, Rotkreuz, Switzerland
| | - N Dhalwani
- Amgen Limited, Cambridge, United Kingdom
| | - G Villa
- Amgen (Europe) GmbH, Rotkreuz, Switzerland
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22
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Gulati U, Ray K, Dasgupta S, Jerusik B. 124 Comparison of First-Pass Peripheral Intravenous Cannulation Using a Handheld Ultrasound Device to Using a Traditional High-End Ultrasound System: A Randomized Controlled Trial. Ann Emerg Med 2021. [DOI: 10.1016/j.annemergmed.2021.09.134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Jana SC, Dutta P, Jain A, Singh A, Adusumilli L, Girotra M, Kumari D, Shirolikar S, Ray K. Kinesin-2 transports Orco into the olfactory cilium of Drosophila melanogaster at specific developmental stages. PLoS Genet 2021; 17:e1009752. [PMID: 34411092 PMCID: PMC8407544 DOI: 10.1371/journal.pgen.1009752] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 08/31/2021] [Accepted: 07/29/2021] [Indexed: 12/21/2022] Open
Abstract
The cilium, the sensing centre for the cell, displays an extensive repertoire of receptors for various cell signalling processes. The dynamic nature of ciliary signalling indicates that the ciliary entry of receptors and associated proteins must be regulated and conditional. To understand this process, we studied the ciliary localisation of the odour-receptor coreceptor (Orco), a seven-pass transmembrane protein essential for insect olfaction. Little is known about when and how Orco gets into the cilia. Here, using Drosophila melanogaster, we show that the bulk of Orco selectively enters the cilia on adult olfactory sensory neurons in two discrete, one-hour intervals after eclosion. A conditional loss of heterotrimeric kinesin-2 during this period reduces the electrophysiological response to odours and affects olfactory behaviour. We further show that Orco binds to the C-terminal tail fragments of the heterotrimeric kinesin-2 motor, which is required to transfer Orco from the ciliary base to the outer segment and maintain within an approximately four-micron stretch at the distal portion of the ciliary outer-segment. The Orco transport was not affected by the loss of critical intraflagellar transport components, IFT172/Oseg2 and IFT88/NompB, respectively, during the adult stage. These results highlight a novel developmental regulation of seven-pass transmembrane receptor transport into the cilia and indicate that ciliary signalling is both developmentally and temporally regulated.
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Affiliation(s)
- Swadhin Chandra Jana
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
- * E-mail: (SCJ); , (KR)
| | - Priya Dutta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Akanksha Jain
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Anjusha Singh
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Lavanya Adusumilli
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Mukul Girotra
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Diksha Kumari
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Seema Shirolikar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- * E-mail: (SCJ); , (KR)
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24
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Harris H, Khera G, Alanbuki AR, Ray K, Yusuf W, Harvey R. 234 Remote Surgical Teaching During COVID-19: Early Feedback from Students and Teachers. Br J Surg 2021. [PMCID: PMC8135698 DOI: 10.1093/bjs/znab134.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Background
On the 23rd March 2020 the government issued a nationwide lockdown in response to COVID-19. Using Microsoft Teams software, Brighton and Sussex Medical School transitioned to remote surgical teaching. We discuss the early feedback from students and tutors.
Method
All students (N = 40) and tutors (N = 7) were invited to complete an online feedback survey.
Results
Twenty students responded. Nine preferred remote teaching. The teaching was described as either good (10/20) or excellent (10/20). Small group teaching, lectures and student lead seminar sessions all received positive feedback. Students preferred sessions that were interactive. One hour was optimal (17/20). There was no consensus over class size. 15/20 (75%) would like remote teaching to continue after the pandemic.
All tutors responded. There was a preference towards shorter sessions: 45 minutes (2/7) one hour (5/7). Tutors found virtual sessions less interactive (6/7). All tutors would like remote teaching to continue after the pandemic. Three suggested extending teaching to remote surgical ward rounds.
Concern was raised by both students and tutors regarding the absence of practical skills.
Conclusions
The value of remote teaching has been highlighted by COVID-19. Our feedback recommends a transition towards blended learning; using the convenience of remote teaching to help augment traditional medical school teaching.
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Affiliation(s)
- H Harris
- oBrighton and Sussex Medical School, Brighton, United Kingdom
| | - G Khera
- oBrighton and Sussex Medical School, Brighton, United Kingdom
| | - A r Alanbuki
- oBrighton and Sussex Medical School, Brighton, United Kingdom
| | - K Ray
- oBrighton and Sussex Medical School, Brighton, United Kingdom
| | - W Yusuf
- oBrighton and Sussex Medical School, Brighton, United Kingdom
| | - R Harvey
- oBrighton and Sussex Medical School, Brighton, United Kingdom
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25
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Kapoor T, Dubey P, Shirolikar S, Ray K. An actomyosin clamp assembled by the Amphiphysin-Rho1-Dia/DAAM-Rok pathway reinforces somatic cell membrane folded around spermatid heads. Cell Rep 2021; 34:108918. [PMID: 33789114 DOI: 10.1016/j.celrep.2021.108918] [Citation(s) in RCA: 3] [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: 08/13/2020] [Revised: 12/22/2020] [Accepted: 03/08/2021] [Indexed: 12/14/2022] Open
Abstract
Membrane curvature recruits Bin-Amphiphysin-Rvs (BAR)-domain proteins and induces local F-actin assembly, which further modifies the membrane curvature and dynamics. The downstream molecular pathway in vivo is still unclear. Here, we show that a tubular endomembrane scaffold supported by contractile actomyosin stabilizes the somatic cyst cell membrane folded around rigid spermatid heads during the final stages of sperm maturation in Drosophila testis. The structure resembles an actin "basket" covering the bundle of spermatid heads. Genetic analyses suggest that the actomyosin organization is nucleated exclusively by the formins - Diaphanous and Dishevelled Associated Activator of Morphogenesis (DAAM) - downstream of Rho1, which is recruited by the BAR-domain protein Amphiphysin. Actomyosin activity at the actin basket gathers the spermatid heads into a compact bundle and resists the somatic cell invasion by intruding spermatids. These observations reveal a distinct response mechanism of actin-membrane interactions, which generates a cell-adhesion-like strategy through active clamping.
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Affiliation(s)
- Tushna Kapoor
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Pankaj Dubey
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Seema Shirolikar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India.
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26
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Garhwal A, Bunruangses M, Arumona AE, Youplao P, Ray K, Suwandee S, Yupapin P. Integrating Metamaterial Antenna Node and LiFi for Privacy Preserving Intelligent COVID-19 Hospital Patient Management. Cognit Comput 2021:1-14. [PMID: 33456619 PMCID: PMC7798388 DOI: 10.1007/s12559-020-09778-6] [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: 07/28/2020] [Accepted: 10/08/2020] [Indexed: 11/16/2022]
Abstract
Light fidelity (LiFi) and wireless fidelity (WiFi) can be applied with the same network under the different constraints, which is suitable for COVID-19 surveillance in hospitals. The LiFi network is a high-capacity and security platform. A COVID-19 surveillance system using LiFi is proposed, which consists of two switching modes: communication and surveillance. Firstly, the communication targets are to accommodate the electromagnetic interference (EMI) immunity and high-capacity and security data transmission, where secondly the COVID-19 surveillance can be applied. In operation, the up and downlink system uses a metamaterial antenna embedded by Mach Zehnder interferometer (MZI). An antenna consists of silver bars embedded at the microring center with two-phase modulators at its sides. The entangled source namely a dark soliton is applied to form the transmission, where the information security based on quantum cryptography can be managed. By using the suitable parameters, the whispering gallery modes (WGMs) are generated and the up and downlink nodes are formed. The input information is multiplexed with time to form the multiplexed signals, where the big data transmission (40 Pbit s - 1 ) can be employed. By using the surveillance mode, the plasmonic antenna can be applied for temperature and electric force sensors, which can offer the disinfectant spray and temperature sensor for COVID-19 applications. The optimum plasma force sensitivity is 0.16 N kg-1 mW-1. The center frequencies of 191.48 THz and 199.41 THz are obtained for uplink and downlink antennas, respectively. The optimum temperature sensitivity is 0.05 rads-1 °C-1. In conclusion, the novelty of proposed work is that the integrated sensor circuits are employed for COVID-19 surveillance in the hospital. The fuzzy-based system is designed for critical patient monitoring alert using this surveillance and management inside the hospital for COVID-19 patients.
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Affiliation(s)
- A. Garhwal
- Amity School of Engineering & Technology, Amity University Rajasthan, Jaipur, 303002 India
| | - M. Bunruangses
- Department of Computer Engineering, Faculty of Industrial Education, Rajamangala University of Technology Phra Nakhon, Bangkok, 10300 Thailand
| | - A. E. Arumona
- Computational Optics Research Group, Advanced Institute of Materials Science, Ton Duc Thang University, District 7, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, District 7, Ho Chi Minh City, Vietnam
- Division of Computational Physics, Institute for Computational Science, Ton Duc Thang University, District 7, Ho Chi Minh City, Vietnam
| | - P. Youplao
- Department of Electrical Engineering, Faculty of Industry and Technology, Rajamangala University of Technology Isan Sakon Nakhon Campus, Sakon Nakhon, 47160 Thailand
| | - K. Ray
- Amity School of Applied Sciences, Amity University Rajasthan, Jaipur, 303002 India
| | - S. Suwandee
- Kasem Bundit University, Bangkok, 10250 Thailand
| | - P. Yupapin
- Faculty of Applied Sciences, Ton Duc Thang University, District 7, Ho Chi Minh City, Vietnam
- Division of Computational Physics, Institute for Computational Science, Ton Duc Thang University, District 7, Ho Chi Minh City, Vietnam
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27
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Villa G, Ray K, Bray S, Catapano A, Poulter N, Vallejo-Vaz A, Brandts J. Comparison of Achieving 2019 ESC/EAS Versus 2018 ACC/AHA LDL-C Goals for Patients with Atherosclerotic Cardiovascular Disease (ASCVD): A Cardiovascular Risk Simulation From the Da Vinci Atudy. Heart Lung Circ 2021. [DOI: 10.1016/j.hlc.2021.06.271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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28
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Tolbert WD, Sherburn R, Gohain N, Ding S, Flinko R, Orlandi C, Ray K, Finzi A, Lewis GK, Pazgier M. Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site. BMC Biol 2020; 18:91. [PMID: 32693837 PMCID: PMC7374964 DOI: 10.1186/s12915-020-00819-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 12/03/2019] [Accepted: 06/22/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The binding of HIV-1 Envelope glycoproteins (Env) to host receptor CD4 exposes vulnerable conserved epitopes within the co-receptor binding site (CoRBS) which are required for the engagement of either CCR5 or CXCR4 co-receptor to allow HIV-1 entry. Antibodies against this region have been implicated in the protection against HIV acquisition in non-human primate (NHP) challenge studies and found to act synergistically with antibodies of other specificities to deliver effective Fc-mediated effector function against HIV-1-infected cells. Here, we describe the structure and function of N12-i2, an antibody isolated from an HIV-1-infected individual, and show how the unique structural features of this antibody allow for its effective Env recognition and Fc-mediated effector function. RESULTS N12-i2 binds within the CoRBS utilizing two adjacent sulfo-tyrosines (TYS) for binding, one of which binds to a previously unknown TYS binding pocket formed by gp120 residues of high sequence conservation among HIV-1 strains. Structural alignment with gp120 in complex with the co-receptor CCR5 indicates that the new pocket corresponds to TYS at position 15 of CCR5. In addition, structure-function analysis of N12-i2 and other CoRBS-specific antibodies indicates a link between modes of antibody binding within the CoRBS and Fc-mediated effector activities. The efficiency of antibody-dependent cellular cytotoxicity (ADCC) correlated with both the level of antibody binding and the mode of antibody attachment to the epitope region, specifically with the way the Fc region was oriented relative to the target cell surface. Antibodies with poor Fc access mediated the poorest ADCC whereas those with their Fc region readily accessible for interaction with effector cells mediated the most potent ADCC. CONCLUSION Our data identify a previously unknown binding site for TYS within the assembled CoRBS of the HIV-1 virus. In addition, our combined structural-modeling-functional analyses provide new insights into mechanisms of Fc-effector function of antibodies against HIV-1, in particular, how antibody binding to Env antigen affects the efficiency of ADCC response.
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Affiliation(s)
- William D Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814-4712, USA
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Rebekah Sherburn
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814-4712, USA
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Neelakshi Gohain
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Shilei Ding
- Centre de Recherche du CHUM, Université de Montréal, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Robin Flinko
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Chiara Orlandi
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Krishanu Ray
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814-4712, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Université de Montréal, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - George K Lewis
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814-4712, USA.
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA.
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29
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Gadre P, Chatterjee S, Varshney B, Ray K. Cyclin E and Cdk1 regulate the termination of germline transit-amplification process in Drosophila testis. Cell Cycle 2020; 19:1786-1803. [PMID: 32573329 DOI: 10.1080/15384101.2020.1780381] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
An extension of the G1 is correlated with stem cell differentiation. The role of cell cycle regulation during the subsequent transit amplification (TA) divisions is, however, unclear. Here, we report for the first time that in the Drosophila male germline lineage, the transit amplification divisions accelerate after the second TA division. The cell cycle phases, marked by Cyclin E and Cyclin B, are progressively altered during the TA. Antagonistic functions of the bag-of-marbles and the Transforming-Growth-Factor-β signaling regulate the cell division rates after the second TA division and the extent of the Cyclin E phase during the fourth TA division. Furthermore, loss of Cyclin E during the fourth TA cycle retards the cell division and induces premature meiosis in some cases. A similar reduction of Cdk1 activity during this stage arrests the penultimate division and subsequent differentiation, whereas enhancement of the Cdk1 activity prolongs the TA by one extra round. Altogether, the results suggest that modification of the cell cycle structure and the rates of cell division after the second TA division determine the extent of amplification. Also, the regulation of the Cyclin E and CDK1 functions during the penultimate TA division determines the induction of meiosis and subsequent differentiation.
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Affiliation(s)
- Purna Gadre
- Department of Biological Sciences, Tata Institute of Fundamental Research , Mumbai, India
| | - Shambhabi Chatterjee
- Department of Biological Sciences, Tata Institute of Fundamental Research , Mumbai, India
| | - Bhavna Varshney
- Department of Biological Sciences, Tata Institute of Fundamental Research , Mumbai, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research , Mumbai, India
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30
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Black LW, Yan B, Ray K. The T4 TerL Prohead Packaging Motor Does Not Drive DNA Translocation by a Proposed Dehydration Mechanism. Viruses 2020; 12:v12050522. [PMID: 32397493 PMCID: PMC7291337 DOI: 10.3390/v12050522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/15/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
A "DNA crunching" linear motor mechanism that employs a grip-and-release transient spring like compression of B- to A-form DNA has been found in our previous studies. Our FRET measurements in vitro show a decrease in distance from TerL to portal during packaging; furthermore, there is a decrease in distance between closely positioned dye pairs in the Y-stem of translocating Y-DNA that conforms to B- and A- structure. In normal translocation into the prohead the TerL motor expels all B-form tightly binding YOYO-1 dye that cannot bind A-form. The TerL motor cannot package A-form dsRNA. Our work reported here shows that addition of helper B form DNA:DNA (D:D) 20mers allows increased packaging of heteroduplex A-form DNA:RNA 20mers (D:R), evidence for a B- to A-form spring motor pushing duplex nucleic acid. A-form DNA:RNA 25mers, 30mers, and 35mers alone are efficiently packaged into proheads by the TerL motor showing that a proposed hypothetical dehydration motor mechanism operating on duplex substrates does not provide the packaging motor force. Taken together with our previous studies showing TerL motor protein motion toward the portal during DNA packaging, our present studies of short D:D and D:R duplex nucleic acid substrates strongly supports our previous evidence that the protein motor pushes rather than pulls or dehydrates duplex substrates to provide the translocation into prohead packaging force.
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Affiliation(s)
- Lindsay W. Black
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (B.Y.); (K.R.)
- Correspondence:
| | - Bingxue Yan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (B.Y.); (K.R.)
| | - Krishanu Ray
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (B.Y.); (K.R.)
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Orlandi C, Deredge D, Ray K, Gohain N, Tolbert W, DeVico AL, Wintrode P, Pazgier M, Lewis GK. Antigen-Induced Allosteric Changes in a Human IgG1 Fc Increase Low-Affinity Fcγ Receptor Binding. Structure 2020; 28:516-527.e5. [PMID: 32209433 DOI: 10.1016/j.str.2020.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 04/24/2019] [Revised: 02/07/2020] [Accepted: 03/05/2020] [Indexed: 11/15/2022]
Abstract
Antibody structure couples adaptive and innate immunity via Fab (antigen binding) and Fc (effector) domains that are connected by unique hinge regions. Because antibodies harbor two or more Fab domains, they are capable of crosslinking multi-determinant antigens, which is required for Fc-dependent functions through associative interactions with effector ligands, including C1q and cell surface Fc receptors. The modular nature of antibodies, with distal ligand binding sites for antigen and Fc-ligands, is reminiscent of allosteric proteins, suggesting that allosteric interactions might contribute to Fc-mediated effector functions. This hypothesis has been pursued for over 40 years and remains unresolved. Here, we provide evidence that allosteric interactions between Fab and Fc triggered by antigen binding modulate binding of Fc to low-affinity Fc receptors (FcγR) for a human IgG1. This work opens the path to further dissection of the relative roles of allosteric and associative interactions in Fc-mediated effector functions.
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Affiliation(s)
- Chiara Orlandi
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Krishanu Ray
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Neelakshi Gohain
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - William Tolbert
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Anthony L DeVico
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Patrick Wintrode
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Marzena Pazgier
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - George K Lewis
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA.
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32
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Ahmed Z, Mazumdar S, Ray K. Kinesin associated protein, DmKAP, binding harnesses the C-terminal ends of the Drosophila kinesin-2 stalk heterodimer. Biochem Biophys Res Commun 2019; 522:506-511. [PMID: 31784087 DOI: 10.1016/j.bbrc.2019.11.111] [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: 11/04/2019] [Accepted: 11/17/2019] [Indexed: 01/01/2023]
Abstract
The heterotrimeric kinesin-2 consists of two distinct motor subunits and an accessory protein, KAP, which binds to the coiled-coil stalk domains and one of the tail domains of the motor subunits. Genetic studies revealed that KAP is essential for the kinesin-2 functions in cilia, flagella, and axon. However, the structural significance of the KAP binding on kinesin-2 assembly and stability is not known. Here, using the Fluorescence Lifetime assay, we show that DmKAP binding selectively reduces the distance between the C-terminal ends of Drosophila kinesin-2 stalk heterodimer. Insertion of a missense mutation (E551K) in the Drosophila kinesin-2α stalk fragment, which was shown to reduce the structural dynamics of the stalk heterodimer earlier, also reduced the distances at both the N- and C-terminal ends of the stalk heterodimer independent of DmKAP. The zipping effect, particularly at the N-terminal end of the mutant stalk heterodimer, is further enhanced in the presence of DmKAP. Together, these results suggest that the KAP binding could alter the structural dynamics of kinesin-2 stalk heterodimer at the C-terminal end and stabilize the association between the stalk domains.
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Affiliation(s)
- Zoheb Ahmed
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Shyamalava Mazumdar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India.
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33
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Affram Y, Zapata JC, Gholizadeh Z, Tolbert WD, Zhou W, Iglesias-Ussel MD, Pazgier M, Ray K, Latinovic OS, Romerio F. The HIV-1 Antisense Protein ASP Is a Transmembrane Protein of the Cell Surface and an Integral Protein of the Viral Envelope. J Virol 2019; 93:e00574-19. [PMID: 31434734 PMCID: PMC6803264 DOI: 10.1128/jvi.00574-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 04/05/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022] Open
Abstract
The negative strand of HIV-1 encodes a highly hydrophobic antisense protein (ASP) with no known homologs. The presence of humoral and cellular immune responses to ASP in HIV-1 patients indicates that ASP is expressed in vivo, but its role in HIV-1 replication remains unknown. We investigated ASP expression in multiple chronically infected myeloid and lymphoid cell lines using an anti-ASP monoclonal antibody (324.6) in combination with flow cytometry and microscopy approaches. At baseline and in the absence of stimuli, ASP shows polarized subnuclear distribution, preferentially in areas with low content of suppressive epigenetic marks. However, following treatment with phorbol 12-myristate 13-acetate (PMA), ASP translocates to the cytoplasm and is detectable on the cell surface, even in the absence of membrane permeabilization, indicating that 324.6 recognizes an ASP epitope that is exposed extracellularly. Further, surface staining with 324.6 and anti-gp120 antibodies showed that ASP and gp120 colocalize, suggesting that ASP might become incorporated in the membranes of budding virions. Indeed, fluorescence correlation spectroscopy studies showed binding of 324.6 to cell-free HIV-1 particles. Moreover, 324.6 was able to capture and retain HIV-1 virions with efficiency similar to that of the anti-gp120 antibody VRC01. Our studies indicate that ASP is an integral protein of the plasma membranes of chronically infected cells stimulated with PMA, and upon viral budding, ASP becomes a structural protein of the HIV-1 envelope. These results may provide leads to investigate the possible role of ASP in the virus replication cycle and suggest that ASP may represent a new therapeutic or vaccine target.IMPORTANCE The HIV-1 genome contains a gene expressed in the opposite, or antisense, direction to all other genes. The protein product of this antisense gene, called ASP, is poorly characterized, and its role in viral replication remains unknown. We provide evidence that the antisense protein, ASP, of HIV-1 is found within the cell nucleus in unstimulated cells. In addition, we show that after PMA treatment, ASP exits the nucleus and localizes on the cell membrane. Moreover, we demonstrate that ASP is present on the surfaces of viral particles. Altogether, our studies identify ASP as a new structural component of HIV-1 and show that ASP is an accessory protein that promotes viral replication. The presence of ASP on the surfaces of both infected cells and viral particles might be exploited therapeutically.
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Affiliation(s)
- Yvonne Affram
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Juan C Zapata
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Zahra Gholizadeh
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - William D Tolbert
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Wei Zhou
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Maria D Iglesias-Ussel
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marzena Pazgier
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Krishanu Ray
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Olga S Latinovic
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Fabio Romerio
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Agrawal P, DeVico AL, Foulke JS, Lewis GK, Pazgier M, Ray K. Stoichiometric Analyses of Soluble CD4 to Native-like HIV-1 Envelope by Single-Molecule Fluorescence Spectroscopy. Cell Rep 2019; 29:176-186.e4. [PMID: 31577947 PMCID: PMC6897359 DOI: 10.1016/j.celrep.2019.08.074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 11/30/2018] [Revised: 06/17/2019] [Accepted: 08/23/2019] [Indexed: 01/14/2023] Open
Abstract
Analyses of HIV-1 envelope (Env) binding to CD4, and the conformational changes the interactions induce, inform the molecular mechanisms and factors governing HIV-1 infection. To address these questions, we used a single-molecule detection (SMD) approach to study the nature of reactions between soluble CD4 (sCD4) and soluble HIV-1 trimers. SMD of these reactions distinguished a mixture of one, two, or three CD4-bound trimer species. Single-ligand trimers were favored at early reaction times and ligand-saturated trimers later. Furthermore, some trimers occupied by one sCD4 molecule did not bind additional ligands, whereas the majority of two ligand-bound species rapidly transitioned to the saturated state. Quantification of liganded trimers observed in reactions with various sCD4 concentrations reflected an overall negative cooperativity in ligand binding. Collectively, our results highlight the general utility of SMD in studying protein interactions and provide critical insights on the nature of sCD4-HIV-1 Env interactions.
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Affiliation(s)
- Parul Agrawal
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Anthony L DeVico
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA; Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - James S Foulke
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - George K Lewis
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Marzena Pazgier
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA.
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35
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Dixit AB, Ray K, Black LW. A viral small terminase subunit (TerS) twin ring pac synapsis DNA packaging model is supported by fluorescent fusion proteins. Virology 2019; 536:39-48. [PMID: 31400548 PMCID: PMC6760839 DOI: 10.1016/j.virol.2019.07.021] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/23/2022]
Abstract
A bacteriophage T4 DNA "synapsis model" proposes that the bacteriophage T4 terminase small subunit (TerS) apposes two pac site containing dsDNA homologs to gauge concatemer maturation adequate for packaging initiation. N-terminus, C-terminus, or both ends modified fusion Ter S proteins retain function. Replacements of the TerS gene in the T4 genome with fusion genes encoding larger (18-45 kDa) TerS-eGFP and TerS-mCherry fluorescent fusion proteins function without significant change in phenotype. Co-infection and co-expression by T4 phages encoding TerS-eGFP and TerS-mCherry shows in vivo FRET in infected bacteria comparable to that of the purified, denatured and then renatured, mixed fusion proteins in vitro. FRET of purified, denatured-renatured, mixed temperature sensitive and native TerS fusion proteins at low and high temperature in vitro shows that TerS ring-like oligomer formation is essential for function in vivo. Super-resolution STORM and PALM microscopy of intercalating dye YOYO-1 DNA and photoactivatable TerS-PAmCherry-C1 fusions support accumulation of TerS dimeric or multiple ring-like oligomer structures containing DNA and gp16-mCherry in vivo as well as in vitro to regulate pac site cutting.
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Affiliation(s)
- Aparna Banerjee Dixit
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Krishanu Ray
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lindsay W Black
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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36
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Ahmed Z, Doodhi H, Bhaumik A, Mazumdar S, Ray K. The structural dynamics of the kinesin-2 stalk heterodimer and its biological relevance. Biochem Biophys Res Commun 2019; 518:171-177. [DOI: 10.1016/j.bbrc.2019.08.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 11/25/2022]
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Abstract
<p><strong>Abstract.</strong> Agricultural production is highly vulnerable to weather extremes. The changing patterns of these extreme events have significant implications on food security. Unprecedented weather extremes can strongly impact crop yield regionally and globally. The present study examines change in the frequency of extreme events (Floods, heat/cold waves, Tropical Cyclones and Lightning) over half a century from 1960 to 2016 and its effects on crop yield over India. The analysis aims at identifying the regions which are more susceptible to extreme events and the changing patterns in the occurrence of these events. Case studies to analyse the influence of the extremes on yields are also attempted for some of the regions with a high frequency of these events.</p>
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38
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Ray K, Mengistu M, Orlandi C, Pazgier M, Lewis GK, DeVico AL. Concurrent Exposure of Neutralizing and Non-neutralizing Epitopes on a Single HIV-1 Envelope Structure. Front Immunol 2019; 10:1512. [PMID: 31338095 PMCID: PMC6628914 DOI: 10.3389/fimmu.2019.01512] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 01/14/2023] Open
Abstract
The trimeric envelope spikes on the HIV-1 virus surface initiate infection and comprise key targets for antiviral humoral responses. Circulating virions variably present intact envelope spikes, which react with neutralizing antibodies; and altered envelope structures, which bind non-neutralizing antibodies. Once bound, either type of antibody can enable humoral effector mechanisms with the potential to control HIV-1 infection in vivo. However, it is not clear how the presentation of neutralizing vs. non-neutralizing epitopes defines distinct virus populations and/or envelope structures on single particles. Here we used single-virion fluorescence correlation spectroscopy (FCS), fluorescence resonance energy transfer (FRET), and two-color coincidence FCS approaches to examine whether neutralizing and non-neutralizing antibodies are presented by the same envelope structure. Given the spatial requirements for donor-acceptor energy transfer (≤10 nm), FRET signals generated by paired neutralizing and non-neutralizing fluorescent Fabs should occur via proximal binding to the same target antigen. Fluorescent-labeled Fabs of the neutralizing anti-gp120 antibodies 2G12 and b12 were combined with Fabs of the non-neutralizing anti-gp41 antibody F240, previously thought to mainly bind gp41 "stumps." We find that both 2G12-F240 and/or b12-F240 Fab combinations generate FRET signals on multiple types of virions in solution. FRET efficiencies position the neutralizing and non-neutralizing epitopes between 7.1 and 7.8 nm apart; potentially fitting within the spatial dimensions of a single trimer-derived structure. Further, the frequency of FRET detection suggests that at least one of such structures occurs on the majority of particles in a virus population. Thus, there is frequent, overlapping presentation of non-neutralizing and neutralizing epitope on freely circulating HIV-1 surfaces. Such information provides a broader perspective of how anti-HIV humoral immunity interfaces with circulating virions.
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Affiliation(s)
- Krishanu Ray
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States,*Correspondence: Krishanu Ray
| | - Meron Mengistu
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Chiara Orlandi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Marzena Pazgier
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - George K. Lewis
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Anthony L. DeVico
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
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39
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Ray K. Improvised 'suture passer': an easy and cost-effective tool for transcorporeal suturing. Ann R Coll Surg Engl 2019; 101:438. [PMID: 31155892 DOI: 10.1308/rcsann.2019.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- K Ray
- Department of General and Gastrointestinal Surgery, Sanjiban Hospital , Fuleshwar, Howrah West Bengal , India
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40
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Orlandi C, Flinko R, Ray K, Hu Y, Mamede J, Maric D, Hope T, Lewis G. PI-4 Trogocytosis of viral immune complexes in the context of HIV-1 infection. J Acquir Immune Defic Syndr 2019. [DOI: 10.1097/01.qai.0000558037.29353.d4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Williams R, Duvall R, Kilaru V, Hagler G, Hassinger L, Benedict K, Rice J, Kaufman A, Judge R, Pierce G, Allen G, Bergin M, Cohen R, Fransioli P, Gerboles M, Habre R, Hannigan M, Jack D, Louie P, Martin N, Penza M, Polidori A, Subramanian R, Ray K, Schauer J, Seto E, Thurston G, Turner J, Wexler A, Ning Z. Deliberating performance targets workshop: Potential paths for emerging PM 2.5 and O 3 air sensor progress. Atmos Environ X 2019; 2:100031. [PMID: 34322666 PMCID: PMC8314253 DOI: 10.1016/j.aeaoa.2019.100031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The United States Environmental Protection Agency held an international two-day workshop in June 2018 to deliberate possible performance targets for non-regulatory fine particulate matter (PM2.5) and ozone (O3) air sensors. The need for a workshop arose from the lack of any market-wide manufacturer requirement for Ozone documented sensor performance evaluations, the lack of any independent third party or government-based sensor performance certification program, and uncertainty among all users as to the general usability of air sensor data. A multi-sector subject matter expert panel was assembled to facilitate an open discussion on these issues with multiple stakeholders. This summary provides an overview of the workshop purpose, key findings from the deliberations, and considerations for future actions specific to sensors. Important findings concerning PM2.5 and O3 sensors included the lack of consistent performance indicators and statistical metrics as well as highly variable data quality requirements depending on the intended use. While the workshop did not attempt to yield consensus on any topic, a key message was that a number of possible future actions would be beneficial to all stakeholders regarding sensor technologies. These included documentation of best practices, sharing quality assurance results along with sensor data, and the development of a common performance target lexicon, performance targets, and test protocols.
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Affiliation(s)
- R. Williams
- U.S. Environmental Protection Agency, Office of Research
and Development, Research Triangle Park, NC, USA
| | - R. Duvall
- U.S. Environmental Protection Agency, Office of Research
and Development, Research Triangle Park, NC, USA
- Corresponding author. U.S. Environmental
Protection Agency, 109 T.W. Alexander Drive, MD E343-02, Research Triangle Park,
NC 27711, USA. (R. Duvall)
| | - V. Kilaru
- U.S. Environmental Protection Agency, Office of Research
and Development, Research Triangle Park, NC, USA
| | - G. Hagler
- U.S. Environmental Protection Agency, Office of Research
and Development, Research Triangle Park, NC, USA
| | - L. Hassinger
- Former Oak Ridge Institute for Science and Education
(ORISE) staff assigned to the U.S. Environmental Protection Agency, Office of
Research and Development, Research Triangle Park, NC, USA
| | - K. Benedict
- U.S. Environmental Protection Agency, Office of Air Quality
Planning and Standards, Research Triangle Park, NC, USA
| | - J. Rice
- U.S. Environmental Protection Agency, Office of Air Quality
Planning and Standards, Research Triangle Park, NC, USA
| | - A. Kaufman
- U.S. Environmental Protection Agency, Office of Air Quality
Planning and Standards, Research Triangle Park, NC, USA
| | - R. Judge
- U.S. Environmental Protection Agency, Region 1, North
Chelmsford, MA, USA
| | - G. Pierce
- Colorado Department of Public Health and the Environment,
Denver, CO, USA
| | - G. Allen
- Northeast States for Coordinated Air Use Management,
Boston, MA, USA
| | - M. Bergin
- Pratt School of Engineering, Duke University, Durham, NC,
USA
| | - R.C. Cohen
- College of Chemistry, University of California-Berkeley,
Berkeley, CA, USA
| | - P. Fransioli
- Clark County Department of Air Quality (Nevada), Las Vegas,
NV, USA
| | - M. Gerboles
- European Commission, Joint Research Centre, Ispra,
Italy
| | - R. Habre
- Keck School of Medicine, University of Southern
California, Los Angeles, CA, USA
| | - M. Hannigan
- Mechanical Engineering Department, University of
Colorado-Boulder, Boulder, CO, USA
| | - D. Jack
- Mailman School of Public Health, Columbia University, New
York, NY, USA
| | - P. Louie
- Hong Kong Environmental Protection Department, Hong Kong,
China
| | - N.A. Martin
- National Physical Laboratory, Teddington, Middlesex,
United Kingdom
| | - M. Penza
- Italian National Agency for New Technologies, Energy and
Sustainable Economic Development (ENEA), Brindisi Research Center, Brindisi,
Italy
- European Network on New Sensing Technologies for
Air-Pollution Control and Environmental Sustainability (EuNetAir), Brindisi,
Italy
| | - A. Polidori
- South Coast Air Quality Management District, Diamond Bar,
CA, USA
| | - R. Subramanian
- Center for Atmospheric Particle Studies, Carnegie Mellon
University, Pittsburgh, PA, USA
| | - K. Ray
- Confederated Tribes of the Colville Reservation, Nespelem,
WAashington, USA
| | - J. Schauer
- College of Engineering, University of Wisconsin-Madison,
Madison, WI, USA
| | - E. Seto
- School of Public Health, University of Washington,
Seattle, WA, USA
| | - G. Thurston
- School of Medicine, New York University, New York, NY,
USA
| | - J. Turner
- School of Engineering and Applied Sciences, Washington
University, St. Louis, MO, USA
| | - A.S. Wexler
- Air Quality Research Center, University of
California-Davis, Davis, CA, USA
| | - Z. Ning
- Hong Kong University of Science and Technology, Hong Kong,
China
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Gupta S, Varshney B, Chatterjee S, Ray K. Somatic ERK activation during transit amplification is essential for maintaining the synchrony of germline divisions in Drosophila testis. Open Biol 2019; 8:rsob.180033. [PMID: 30045884 PMCID: PMC6070716 DOI: 10.1098/rsob.180033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 02/18/2018] [Accepted: 06/28/2018] [Indexed: 12/23/2022] Open
Abstract
Transit amplification (TA) of progenitor cells maintains tissue homeostasis by balancing proliferation and differentiation. In Drosophila testis, the germline proliferation is tightly regulated by factors present in both the germline and the neighbouring somatic cyst cells (SCCs). Although the exact mechanism is unclear, the epidermal growth factor receptor (EGFR) activation in SCCs has been reported to control spermatogonial divisions within a cyst, through downstream activations of Rac1-dependent pathways. Here, we report that somatic activation of the mitogen-activated protein kinase (Rolled/ERK) downstream of EGFR is required to synchronize the mitotic divisions and regulate the transition to meiosis. The process operates independently of the Bag-of-marble activity in the germline. Also, the integrity of the somatic cyst enclosure is inessential for this purpose. Together, these results suggest that synchronization of germ-cell divisions through somatic activation of distinct ERK-downstream targets independently regulates TA and subsequent differentiation of neighbouring germline cells.
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Affiliation(s)
- Samir Gupta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Bhavana Varshney
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Shambhabi Chatterjee
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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Dubey P, Kapoor T, Gupta S, Shirolikar S, Ray K. Atypical septate junctions maintain the somatic enclosure around maturing spermatids and prevent premature sperm release in Drosophila testis. Biol Open 2019; 8:bio.036939. [PMID: 30635267 PMCID: PMC6398457 DOI: 10.1242/bio.036939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Indexed: 01/06/2023] Open
Abstract
Tight junctions prevent paracellular flow and maintain cell polarity in an epithelium. These junctions are also required for maintaining the blood-testis barrier, which is essential for sperm differentiation. Septate junctions in insects are orthologous to the tight junctions. In Drosophila testis, major septate junction components co-localize at the interface of germline and somatic cells initially, and then condense between the two somatic cells in a cyst after germline meiosis. Their localization is extensively remodeled in subsequent stages. We find that characteristic septate junctions are formed between the somatic cyst cells at the elongated spermatid stage. Consistent with previous reports, knockdown of essential junctional components – Discs-large-1 and Neurexin-IV – during the early stages disrupted sperm differentiation beyond the spermatocyte stage. Knockdown of these proteins during the final stages of spermatid maturation caused premature release of spermatids inside the testes, resulting in partial loss of male fertility. These results indicate the importance of maintaining the integrity of the somatic enclosure during spermatid coiling and release in Drosophila testis. It also highlights the functional similarity with the tight junction proteins during mammalian spermatogenesis. This article has an associated First Person interview with the first author of the paper. Summary: Septate junctions seal the somatic enclosure around maturing spermatids in Drosophila testis. The junction integrity, maintained by Dlg1 and NrxIV, is essential for keeping the somatic enclosure intact until the mature spermatids are released.
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Affiliation(s)
- Pankaj Dubey
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Tushna Kapoor
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Samir Gupta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Seema Shirolikar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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44
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Gerschel P, Warm K, Farquhar ER, Englert U, Reback ML, Siegmund D, Ray K, Apfel UP. Sulfur substitution in a Ni(cyclam) derivative results in lower overpotential for CO 2 reduction and enhanced proton reduction. Dalton Trans 2019; 48:5923-5932. [PMID: 30624449 DOI: 10.1039/c8dt04740e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The replacement of the opposing nitrogen atoms in 1,4,8,11-tetraazacyclotetradecane (cyclam) with two sulfur atoms in 1,8-dithia-4,11-diazacyclotetradecane (dithiacyclam) enables the electrochemical reduction of protons and CO2via the corresponding nickel(ii) complex at more positive potentials. In addition, a 10-fold enhancement in the proton reduction rate of [Ni(dithiacyclam)]2+ relative to [Ni(cylcam)]2+ was observed. The study provides vital insight into Nature's choice of employing predominantly sulfur based ligand platforms in achieving biological proton and CO2 reductions.
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Affiliation(s)
- P Gerschel
- Ruhr-Universität Bochum, Anorganische Chemie I, Universitätsstraße 150, 44801 Bochum, Germany.
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45
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Ray K, Bruckert E, Annemans L, Van Hout B, Schoonen M, Bridges I. P1699Characteristics of patients prescribed Evolocumab in Europe. Does clinical use match clinical guidelines? Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p1699] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- K Ray
- Imperial College London, London, United Kingdom
| | - E Bruckert
- Hospital Pitie-Salpetriere, Paris, France
| | | | - B Van Hout
- University of Sheffield, Sheffield, United Kingdom
| | | | - I Bridges
- Amgen Ltd., Cambridge, United Kingdom
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Dey S, Ray K. Cholinergic activity is essential for maintaining the anterograde transport of Choline Acetyltransferase in Drosophila. Sci Rep 2018; 8:8028. [PMID: 29795337 PMCID: PMC5966444 DOI: 10.1038/s41598-018-26176-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 10/24/2017] [Accepted: 04/30/2018] [Indexed: 12/14/2022] Open
Abstract
Cholinergic activity is essential for cognitive functions and neuronal homeostasis. Choline Acetyltransferase (ChAT), a soluble protein that synthesizes acetylcholine at the presynaptic compartment, is transported in bulk in the axons by the heterotrimeric Kinesin-2 motor. Axonal transport of soluble proteins is described as a constitutive process assisted by occasional, non-specific interactions with moving vesicles and motor proteins. Here, we report that an increase in the influx of Kinesin-2 motor and association between ChAT and the motor during a specific developmental period enhances the axonal entry, as well as the anterograde flow of the protein, in the sensory neurons of intact Drosophila nervous system. Loss of cholinergic activity due to Hemicholinium and Bungarotoxin treatments, respectively, disrupts the interaction between ChAT and Kinesin-2 in the axon, and the episodic enhancement of axonal influx of the protein. Altogether, these observations highlight a phenomenon of synaptic activity-dependent, feedback regulation of a soluble protein transport in vivo, which could potentially define the quantum of its pre-synaptic influx.
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Affiliation(s)
- Swagata Dey
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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Rai D, Dey S, Ray K. A method for estimating relative changes in the synaptic density in Drosophila central nervous system. BMC Neurosci 2018; 19:30. [PMID: 29769037 PMCID: PMC5956817 DOI: 10.1186/s12868-018-0430-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 08/17/2017] [Accepted: 05/02/2018] [Indexed: 12/16/2022] Open
Abstract
Background Synapse density is an essential indicator of development and functioning of the central nervous system. It is estimated indirectly through the accumulation of pre and postsynaptic proteins in tissue sections. 3D reconstruction of the electron microscopic images in serial sections is one of the most definitive means of estimating the formation of active synapses in the brain. It is tedious and highly skill-dependent. Confocal imaging of whole mounts or thick sections of the brain provides a natural alternative for rapid gross estimation of the synapse density in large areas. The optical resolution and other deep-tissue imaging aberrations limit the quantitative scope of this technique. Results Here we demonstrate a simple sample preparation method that could enhance the clarity of the confocal images of the neuropil regions of the ventral nerve cord of Drosophila larvae, providing a clear view of synapse distributions. We estimated the gross volume occupied by the synaptic junctions using 3D object counter plug-in of Fiji/ImageJ®. It gave us a proportional estimate of the number of synaptic junctions in the neuropil region. The method is corroborated by correlated super-resolution imaging analysis and through genetic perturbation of synaptogenesis in the larval brain. Conclusions The method provides a significant improvement in the relative estimate of region-specific synapse density in the central nervous system. Also, it reduced artifacts in the super-resolution images obtained using the stimulated emission depletion microscopy technique. Electronic supplementary material The online version of this article (10.1186/s12868-018-0430-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dipti Rai
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Swagata Dey
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India.
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48
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Dey S, Banker G, Ray K. Anterograde Transport of Rab4-Associated Vesicles Regulates Synapse Organization in Drosophila. Cell Rep 2017; 18:2452-2463. [PMID: 28273459 DOI: 10.1016/j.celrep.2017.02.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 04/18/2016] [Revised: 12/19/2016] [Accepted: 02/09/2017] [Indexed: 11/29/2022] Open
Abstract
Local endosomal recycling at synapses is essential to maintain neurotransmission. Rab4GTPase, found on sorting endosomes, is proposed to balance the flow of vesicles among endocytic, recycling, and degradative pathways in the presynaptic compartment. Here, we report that Rab4-associated vesicles move bidirectionally in Drosophila axons but with an anterograde bias, resulting in their moderate enrichment at the synaptic region of the larval ventral ganglion. Results from FK506 binding protein (FKBP) and FKBP-Rapamycin binding domain (FRB) conjugation assays in rat embryonic fibroblasts together with genetic analyses in Drosophila indicate that an association with Kinesin-2 (mediated by the tail domain of Kinesin-2α/KIF3A/KLP64D subunit) moves Rab4-associated vesicles toward the synapse. Reduction in the anterograde traffic of Rab4 causes an expansion of the volume of the synapse-bearing region in the ventral ganglion and increases the motility of Drosophila larvae. These results suggest that Rab4-dependent vesicular traffic toward the synapse plays a vital role in maintaining synaptic balance in this neuronal network.
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Affiliation(s)
- Swagata Dey
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India.
| | - Gary Banker
- Jungers Center for Neurosciences Research, Oregon Health and Science University, Portland, OR 97239, USA
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India.
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Tolbert WD, Gohain N, Alsahafi N, Van V, Orlandi C, Ding S, Martin L, Finzi A, Lewis GK, Ray K, Pazgier M. Targeting the Late Stage of HIV-1 Entry for Antibody-Dependent Cellular Cytotoxicity: Structural Basis for Env Epitopes in the C11 Region. Structure 2017; 25:1719-1731.e4. [PMID: 29056481 PMCID: PMC5677539 DOI: 10.1016/j.str.2017.09.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 07/18/2017] [Revised: 08/28/2017] [Accepted: 09/18/2017] [Indexed: 01/14/2023]
Abstract
Antibodies can have an impact on HIV-1 infection in multiple ways, including antibody-dependent cellular cytotoxicity (ADCC), a correlate of protection observed in the RV144 vaccine trial. One of the most potent ADCC-inducing epitopes on HIV-1 Env is recognized by the C11 antibody. Here, we present the crystal structure, at 2.9 Å resolution, of the C11-like antibody N12-i3, in a quaternary complex with the HIV-1 gp120, a CD4-mimicking peptide M48U1, and an A32-like antibody, N5-i5. Antibody N12-i3 recognizes an epitope centered on the N-terminal "eighth strand" of a critical β sandwich, which our analysis indicates to be emblematic of a late-entry state, after the gp120 detachment. In prior entry states, this sandwich comprises only seven strands, with the eighth strand instead pairing with a portion of the gp120 C terminus. The conformational gymnastics of HIV-1 gp120 thus includes altered β-strand pairing, possibly to reduce immunogenicity, although nevertheless still recognized by the human immune system.
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Affiliation(s)
- William D. Tolbert
- Division of Vaccine Research, Institute of Human Virology, Biology of University of Maryland School of Medicine, Baltimore, USA,Department of Biochemistry and Molecular, Biology of University of Maryland School of Medicine, Baltimore, USA
| | - Neelakshi Gohain
- Division of Vaccine Research, Institute of Human Virology, Biology of University of Maryland School of Medicine, Baltimore, USA,Department of Biochemistry and Molecular, Biology of University of Maryland School of Medicine, Baltimore, USA
| | - Nirmin Alsahafi
- Centre de Recherche du CHUM, Université de Montréal, Montreal, Quebec, Canada,CEA, Joliot, Service d’Ingénierie Moléculaire des Protéines, F-91191 Gif-sur-Yvette, France
| | - Verna Van
- Division of Vaccine Research, Institute of Human Virology, Biology of University of Maryland School of Medicine, Baltimore, USA,Department of Biochemistry and Molecular, Biology of University of Maryland School of Medicine, Baltimore, USA
| | - Chiara Orlandi
- Division of Vaccine Research, Institute of Human Virology, Biology of University of Maryland School of Medicine, Baltimore, USA,Department of Microbiology and Immunology of University of Maryland School of Medicine, Baltimore, USA
| | - Shilei Ding
- Centre de Recherche du CHUM, Université de Montréal, Montreal, Quebec, Canada,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Loïc Martin
- CEA, Joliot, Service d’Ingénierie Moléculaire des Protéines, F-91191 Gif-sur-Yvette, France
| | - Andrés Finzi
- Centre de Recherche du CHUM, Université de Montréal, Montreal, Quebec, Canada,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada,Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - George K. Lewis
- Division of Vaccine Research, Institute of Human Virology, Biology of University of Maryland School of Medicine, Baltimore, USA,Department of Microbiology and Immunology of University of Maryland School of Medicine, Baltimore, USA
| | - Krishanu Ray
- Department of Biochemistry and Molecular, Biology of University of Maryland School of Medicine, Baltimore, USA
| | - Marzena Pazgier
- Division of Vaccine Research, Institute of Human Virology, Biology of University of Maryland School of Medicine, Baltimore, USA,Department of Biochemistry and Molecular, Biology of University of Maryland School of Medicine, Baltimore, USA,To whom correspondence should be addressed: , 725 West Lombard Street, Baltimore, MD 21201, USA, Tel: (410) 706-4780, Fax: (410) 706-7583
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Perez A, Ray K, Turner A, Cook N, Cerminara K, Suciu G, Cohn Steinkohl D. IMPROVING END-OF-LIFE CARE FOR MINORITIES IN SOUTH FLORIDA: KNOWLEDGE, CHOICES, AND POLICIES. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- A.M. Perez
- College of Osteopathic Medicine, Master of Public Health program, Nova Southeastern University, Ft. Lauderdale, Florida,
| | - K. Ray
- College of Osteopathic Medicine, Master of Public Health program, Nova Southeastern University, Ft. Lauderdale, Florida,
| | - A. Turner
- College of Health Care Sciences, Nova Southeastern University, Ft. Lauderdale, Florida,
| | - N. Cook
- College of Osteopathic Medicine, Master of Public Health program, Nova Southeastern University, Ft. Lauderdale, Florida,
| | - K. Cerminara
- Shepard Broad College of Law, Nova Southeastern University, Ft. Lauderdale, Florida
| | - G. Suciu
- College of Osteopathic Medicine, Master of Public Health program, Nova Southeastern University, Ft. Lauderdale, Florida,
| | - D. Cohn Steinkohl
- College of Osteopathic Medicine, Master of Public Health program, Nova Southeastern University, Ft. Lauderdale, Florida,
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