1
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Feng W, Beer JC, Hao Q, Ariyapala IS, Sahajan A, Komarov A, Cha K, Moua M, Qiu X, Xu X, Iyengar S, Yoshimura T, Nagaraj R, Wang L, Yu M, Engel K, Zhen L, Xue W, Lee CJ, Park CH, Peng C, Zhang K, Grzybowski A, Hahm J, Schmidt SV, Odainic A, Spitzer J, Buddika K, Kuo D, Fang L, Zhang B, Chen S, Latz E, Yin Y, Luo Y, Ma XJ. NULISA: a proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing. Nat Commun 2023; 14:7238. [PMID: 37945559 PMCID: PMC10636041 DOI: 10.1038/s41467-023-42834-x] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
The blood proteome holds great promise for precision medicine but poses substantial challenges due to the low abundance of most plasma proteins and the vast dynamic range of the plasma proteome. Here we address these challenges with NUcleic acid Linked Immuno-Sandwich Assay (NULISA™), which improves the sensitivity of traditional proximity ligation assays by ~10,000-fold to attomolar level, by suppressing assay background via a dual capture and release mechanism built into oligonucleotide-conjugated antibodies. Highly multiplexed quantification of both low- and high-abundance proteins spanning a wide dynamic range is achieved by attenuating signals from abundant targets with unconjugated antibodies and next-generation sequencing of barcoded reporter DNA. A 200-plex NULISA containing 124 cytokines and chemokines and other proteins demonstrates superior sensitivity to a proximity extension assay in detecting biologically important low-abundance biomarkers in patients with autoimmune diseases and COVID-19. Fully automated NULISA makes broad and in-depth proteomic analysis easily accessible for research and diagnostic applications.
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Affiliation(s)
- Wei Feng
- Alamar Biosciences, Inc, Fremont, CA, USA
| | | | - Qinyu Hao
- Alamar Biosciences, Inc, Fremont, CA, USA
| | | | | | | | - Katie Cha
- Alamar Biosciences, Inc, Fremont, CA, USA
| | - Mason Moua
- Alamar Biosciences, Inc, Fremont, CA, USA
| | | | - Xiaomei Xu
- Alamar Biosciences, Inc, Fremont, CA, USA
| | | | | | | | - Li Wang
- Alamar Biosciences, Inc, Fremont, CA, USA
| | - Ming Yu
- Alamar Biosciences, Inc, Fremont, CA, USA
| | - Kate Engel
- Alamar Biosciences, Inc, Fremont, CA, USA
| | - Lucas Zhen
- Alamar Biosciences, Inc, Fremont, CA, USA
| | - Wen Xue
- Alamar Biosciences, Inc, Fremont, CA, USA
| | | | | | - Cheng Peng
- Alamar Biosciences, Inc, Fremont, CA, USA
| | | | | | | | - Susanne V Schmidt
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Alexandru Odainic
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Jasper Spitzer
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | | | - Dwight Kuo
- Alamar Biosciences, Inc, Fremont, CA, USA
| | - Lei Fang
- Alamar Biosciences, Inc, Fremont, CA, USA
| | | | - Steve Chen
- Alamar Biosciences, Inc, Fremont, CA, USA
| | - Eicke Latz
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), Berlin, Germany
| | - Yiyuan Yin
- Alamar Biosciences, Inc, Fremont, CA, USA
| | - Yuling Luo
- Alamar Biosciences, Inc, Fremont, CA, USA.
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2
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Huang Y, Arab T, Russell AE, Mallick ER, Nagaraj R, Gizzie E, Redding‐Ochoa J, Troncoso JC, Pletnikova O, Turchinovich A, Routenberg DA, Witwer KW. Toward a human brain extracellular vesicle atlas: Characteristics of extracellular vesicles from different brain regions, including small RNA and protein profiles. Interdiscip Med 2023; 1:e20230016. [PMID: 38089920 PMCID: PMC10712435 DOI: 10.1002/inmd.20230016] [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] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 12/20/2023]
Abstract
Extracellular vesicles (EVs) are released from different cell types in the central nervous system (CNS) and play roles in regulating physiological and pathological functions. Although brain-derived EVs (bdEVs) have been successfully collected from brain tissue, there is not yet a "bdEV Atlas" of EVs from different brain regions. To address this gap, we separated EVs from eight anatomical brain regions of a single individual and subsequently characterized them by count, size, morphology, and protein and RNA content. The greatest particle yield was from cerebellum, while the fewest particles were recovered from the orbitofrontal, postcentral gyrus, and thalamus regions. EV surface phenotyping indicated that CD81 and CD9 were more abundant than CD63 in all regions. Cell-enriched surface markers varied between brain regions. For example, putative neuronal markers NCAM, CD271, and NRCAM were more abundant in medulla, cerebellum, and occipital regions, respectively. These findings, while restricted to tissues from a single individual, suggest that additional studies are warranted to provide more insight into the links between EV heterogeneity and function in the CNS.
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Affiliation(s)
- Yiyao Huang
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Tanina Arab
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Ashley E. Russell
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of BiologySchool of SciencePenn State ErieThe Behrend CollegeEriePennsylvaniaUSA
| | - Emily R. Mallick
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | | | - Evan Gizzie
- Meso Scale DiagnosticsLLCRockvilleMarylandUSA
| | - Javier Redding‐Ochoa
- Department of PathologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Juan C. Troncoso
- Department of PathologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Olga Pletnikova
- Department of PathologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Pathology and Anatomical SciencesJacobs School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNew YorkUSA
| | - Andrey Turchinovich
- Division of Cancer Genome ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Heidelberg Biolabs GmbHHeidelbergGermany
| | | | - Kenneth W. Witwer
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer's DiseaseJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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3
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Feng W, Beer J, Hao Q, Ariyapala IS, Sahajan A, Komarov A, Cha K, Moua M, Qiu X, Xu X, Iyengar S, Yoshimura T, Nagaraj R, Wang L, Yu M, Engel K, Zhen L, Xue W, Lee CJ, Park CH, Peng C, Zhang K, Grzybowski A, Hahm J, Schmidt SV, Odainic A, Spitzer J, Buddika K, Kuo D, Fang L, Zhang B, Chen S, Latz E, Yin Y, Luo Y, Ma XJ. NULISA: a novel proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing. bioRxiv 2023:2023.04.09.536130. [PMID: 37090549 PMCID: PMC10120728 DOI: 10.1101/2023.04.09.536130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The blood proteome holds great promise for precision medicine but poses substantial challenges due to the low abundance of most plasma proteins and the vast dynamic range across the proteome. We report a novel proteomic technology - NUcleic acid Linked Immuno-Sandwich Assay (NULISA™) - that incorporates a dual capture and release mechanism to suppress the assay background and improves the sensitivity of the proximity ligation assay by over 10,000-fold to the attomolar level. It utilizes pairs of antibodies conjugated to DNA oligonucleotides that enable immunocomplex purification and generate reporter DNA containing target- and sample-specific barcodes for a next-generation sequencing-based, highly multiplexed readout. A 200-plex NULISA targeting 124 cytokines and chemokines and 80 other immune response-related proteins demonstrated superior sensitivity for detecting low-abundance proteins and high concordance with other immunoassays. The ultrahigh sensitivity allowed the detection of previously difficult-to-detect, but biologically important, low-abundance biomarkers in patients with autoimmune diseases and COVID-19. Fully automated NULISA addresses longstanding challenges in proteomic analysis of liquid biopsies and makes broad and in-depth proteomic analysis accessible to the general research community and future diagnostic applications.
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4
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Huang Y, Arab T, Russell AE, Mallick ER, Nagaraj R, Gizzie E, Redding-Ochoa J, Troncoso JC, Pletnikova O, Turchinovich A, Routenberg DA, Witwer KW. Towards a human brain EV atlas: Characteristics of EVs from different brain regions, including small RNA and protein profiles. bioRxiv 2023:2023.05.06.539665. [PMID: 37214955 PMCID: PMC10197569 DOI: 10.1101/2023.05.06.539665] [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: 05/24/2023]
Abstract
Extracellular vesicles (EVs) are released from different cell types in the central nervous system (CNS) and play roles in regulating physiological and pathological functions. Although brain-derived EVs (bdEVs) have been successfully collected from brain tissue, there is not yet a "bdEV atlas" of EVs from different brain regions. To address this gap, we separated EVs from eight anatomical brain regions of a single individual and subsequently characterized them by count, size, morphology, and protein and RNA content. The greatest particle yield was from cerebellum, while the fewest particles were recovered from the orbitofrontal, postcentral gyrus, and thalamus regions. EV surface phenotyping indicated that CD81 and CD9 were more abundant than CD63 for all regions. Cell-enriched surface markers varied between brain regions. For example, putative neuronal markers NCAM, CD271, and NRCAM were more abundant in medulla, cerebellum, and occipital regions, respectively. These findings, while restricted to tissues from a single individual, suggest that additional studies are merited to lend more insight into the links between EV heterogeneity and function in the CNS.
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Affiliation(s)
- Yiyao Huang
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tanina Arab
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ashley E. Russell
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biology, School of Science, Penn State Erie, The Behrend College, Erie, PA, United States
| | - Emily R. Mallick
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Evan Gizzie
- Meso Scale Diagnostics, LLC, Rockville, MD, USA
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Juan C. Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Andrey Turchinovich
- Division of Cancer Genome Research, German Cancer Research Center DKFZ, Heidelberg, Germany
- Heidelberg Biolabs GmbH, Mannheim, Germany
| | | | - Kenneth W. Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD, US
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5
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Jiji C, Nagaraj R, Maikandavel V. ASALD: adaptive sparse augmented lagrangian deblurring of underwater images with optical priori. The Imaging Science Journal 2023. [DOI: 10.1080/13682199.2023.2173546] [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] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Chrispin Jiji
- Department of Electronics and Communication, The Oxford College of Engineering, Bangalore, Karnataka, India
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6
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Huang Y, Driedonks TAP, Cheng L, Rajapaksha H, Turchinovich A, Routenberg DA, Nagaraj R, Redding-Ochoa J, Arab T, Powell BH, Pletnikova O, Troncoso JC, Zheng L, Hill AF, Mahairaki V, Witwer KW. Relationships of APOE Genotypes With Small RNA and Protein Cargo of Brain Tissue Extracellular Vesicles From Patients With Late-Stage AD. Neurol Genet 2022; 8:e200026. [PMID: 36405397 PMCID: PMC9667865 DOI: 10.1212/nxg.0000000000200026] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022]
Abstract
Background and Objectives Variants of the apolipoprotein E (APOE) gene are the greatest known risk factors for sporadic Alzheimer disease (AD). Three major APOE isoform alleles, ε2, ε3, and ε4, encode and produce proteins that differ by only 1-2 amino acids but have different binding partner interactions. Whereas APOE ε2 is protective against AD relative to ε3, ε4 is associated with an increased risk for AD development. However, the role of APOE in gene regulation in AD pathogenesis has remained largely undetermined. Extracellular vesicles (EVs) are lipid bilayer-delimited particles released by cells to dispose of unwanted materials and mediate intercellular communication, and they are implicated in AD pathophysiology. Brain-derived EVs (bdEVs) could act locally in the tissue and reflect cellular changes. To reveal whether APOE genotype affects EV components in AD brains, bdEVs were separated from patients with AD with different APOE genotypes for parallel small RNA and protein profile. Methods bdEVs from late-stage AD brains (BRAAK stages 5-6) from patients with APOE genotypes ε2/3 (n = 5), ε3/3 (n = 5), ε3/4 (n = 6), and ε4/4 (n = 6) were separated using our published protocol into a 10,000g pelleted extracellular fraction (10K) and a further purified EV fraction. Counting, sizing, and multiomic characterization by small RNA sequencing and proteomic analysis were performed for 10K, EVs, and source tissue. Results Comparing APOE genotypes, no significant differences in bdEV total particle concentration or morphology were observed. Overall small RNA and protein profiles of 10K, EVs, and source tissue also did not differ substantially between different APOE genotypes. However, several differences in individual RNAs (including miRNAs and tRNAs) and proteins in 10K and EVs were observed when comparing the highest and lowest risk groups (ε4/4 and ε2/3). Bioinformatic analysis and previous publications indicate a potential regulatory role of these molecules in AD. Discussion For patients with late-stage AD in this study, only a few moderate differences were observed for small RNA and protein profiles between APOE genotypes. Among these, several newly identified 10K and EV-associated molecules may play roles in AD progression. Possibly, larger genotype-related differences exist and are more apparent in or before earlier disease stages.
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Affiliation(s)
- Yiyao Huang
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tom A P Driedonks
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lesley Cheng
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Harinda Rajapaksha
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Andrey Turchinovich
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - David A Routenberg
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Rajini Nagaraj
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Javier Redding-Ochoa
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tanina Arab
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Bonita H Powell
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Olga Pletnikova
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Juan C Troncoso
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lei Zheng
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Andrew F Hill
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Vasiliki Mahairaki
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology (Y.H., T.A.P.D., T.A., B.H.P., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Biochemistry and Chemistry (L.C., H.R., A.F.H.), La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia; Molecular Epidemiology (A.T.), German Cancer Research Center DKFZ, Heidelberg, Germany; SciBerg e.Kfm (A.T.), Mannheim, Germany; Meso Scale Diagnostics (D.A.R., R.N.), LLC, Rockville, MD; Department of Pathology (J.R.-O., O.P., J.C.T.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology and Anatomical Sciences (O.P.), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY; Department of Neurology (J.C.T., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD; Department of Laboratory Medicine (L.Z.), Institute of Health and Sport (A.F.H.), Victoria University, Melbourne, Australia; Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Genetic Medicine (V.M.); and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease (V.M., K.W.W.), Johns Hopkins University School of Medicine, Baltimore, MD
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7
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Spanos M, Shachar S, Sweeney T, Lehmann HI, Gokulnath P, Li G, Sigal GB, Nagaraj R, Bathala P, Rana F, Shah RV, Routenberg DA, Das S. Elevation of neural injury markers in patients with neurologic sequelae after hospitalization for SARS-CoV-2 infection. iScience 2022; 25:104833. [PMID: 35937088 PMCID: PMC9341164 DOI: 10.1016/j.isci.2022.104833] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/08/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Patients with SARS-CoV-2 infection (COVID-19) risk developing long-term neurologic symptoms after infection. Here, we identify biomarkers associated with neurologic sequelae one year after hospitalization for SARS-CoV-2 infection. SARS-CoV-2-positive patients were followed using post-SARS-CoV-2 online questionnaires and virtual visits. Hospitalized adults from the pre-SARS-CoV-2 era served as historical controls. 40% of hospitalized patients develop neurological sequelae in the year after recovery from acute COVID-19 infection. Age, disease severity, and COVID-19 infection itself was associated with additional risk for neurological sequelae in our cohorts. Glial fibrillary astrocytic protein (GFAP) and neurofilament light chain (NF-L) were significantly elevated in SARS-CoV-2 infection. After adjusting for age, sex, and disease severity, GFAP and NF-L remained significantly associated with longer term neurological symptoms in patients with SARS-CoV-2 infection. GFAP and NF-L warrant exploration as biomarkers for long-term neurologic complications after SARS-CoV-2 infection.
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Affiliation(s)
- Michail Spanos
- Cardiovascular Research Center, 185 Cambridge Street, Simches 3 Massachusetts General Hospital, Boston, MA, USA
| | - Sigal Shachar
- Meso Scale Diagnostics, LLC. (MSD), Rockville, MD, USA
| | - Thadryan Sweeney
- Cardiovascular Research Center, 185 Cambridge Street, Simches 3 Massachusetts General Hospital, Boston, MA, USA
| | - H. Immo Lehmann
- Cardiovascular Research Center, 185 Cambridge Street, Simches 3 Massachusetts General Hospital, Boston, MA, USA
| | - Priyanka Gokulnath
- Cardiovascular Research Center, 185 Cambridge Street, Simches 3 Massachusetts General Hospital, Boston, MA, USA
| | - Guoping Li
- Cardiovascular Research Center, 185 Cambridge Street, Simches 3 Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | - Farhan Rana
- Cardiovascular Research Center, 185 Cambridge Street, Simches 3 Massachusetts General Hospital, Boston, MA, USA
| | - Ravi V. Shah
- Cardiovascular Research Center, 185 Cambridge Street, Simches 3 Massachusetts General Hospital, Boston, MA, USA
| | | | - Saumya Das
- Cardiovascular Research Center, 185 Cambridge Street, Simches 3 Massachusetts General Hospital, Boston, MA, USA
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8
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Nagaraj R, Rajagopal V, Raja A, Ranjith S. Influence of Dy 3+ ion concentration on photoluminescence and energy transfer mechanism of promising KBaScSi 3O 9 phosphors for warm white LEDs. Spectrochim Acta A Mol Biomol Spectrosc 2022; 264:120212. [PMID: 34358785 DOI: 10.1016/j.saa.2021.120212] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/11/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
A novel white light emitting silicate-based phosphor of Dy3+ activated KBaScSi3O9 (xDyKBS) was prepared by a conventional solid state method. Powder X-ray diffraction patterns represent the pure phase of synthesized materials that was formed with monoclinic structure. The metal-ligand bonding nature and electronic band structure have been examined optical absorption spectra. The luminescence emission curves of the silicate phosphors display an intense yellow emission peak at 579 nm and a blue emission peak at 491 nm. Among the emission bands, the band observed in the yellow region due to 4F9/2→6H13/2 transition was found to be higher intensity. The radiative parameters like transition probabilities (AR), branching ratios (βR) and stimulated emission cross-section (σPE) values were calculated using Judd-Ofelt parameters and refractive index values for the observed transitions in emission spectra. The life time measurements were made for 4F9/2 → 6H13/2 transition of all the studied samples by keeping an excitation at 350 nm and emission at 579 nm and decay curves were fitted to bi-exponential fitting method. The CCT values obtained from the color coordinates suggested that present xDyKBS phosphors can emit warm and neutral white light depending upon the dopant concentration under near-UV excitation. Our results demonstrated that the optimum concentration 0.05DyKBS phosphor can be successfully utilized as a promising and potential candidate for various innovative photonic applications like warm white LEDs, solar cells, optical sensors and lasers.
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Affiliation(s)
- R Nagaraj
- Department of Physics, SRM Institute of Science and Technology, Ramapuram Campus, Bharathi Salai, Ramapuram, Chennai, TN 89, India
| | | | - Arumugam Raja
- SSN Research Centre, SSN College of Engineering, Chennai 603 110, India
| | - S Ranjith
- Department of Physics, SRM Institute of Science and Technology, Ramapuram Campus, Bharathi Salai, Ramapuram, Chennai, TN 89, India.
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9
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Huang Y, Driedonks TA, Cheng L, Rajapaksha H, Routenberg DA, Nagaraj R, Redding J, Arab T, Powell BH, Pletniková O, Troncoso JC, Zheng L, Hill AF, Mahairaki V, Witwer KW. Brain Tissue-Derived Extracellular Vesicles in Alzheimer's Disease Display Altered Key Protein Levels Including Cell Type-Specific Markers. J Alzheimers Dis 2022; 90:1057-1072. [PMID: 36213994 PMCID: PMC9741741 DOI: 10.3233/jad-220322] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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] [Accepted: 09/02/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Brain tissue-derived extracellular vesicles (bdEVs) play neurodegenerative and protective roles, including in Alzheimer's disease (AD). Extracellular vesicles (EVs) may also leave the brain to betray the state of the CNS in the periphery. Only a few studies have profiled the proteome of bdEVs and source brain tissue. Additionally, studies focusing on bdEV cell type-specific surface markers are rare. OBJECTIVE We aimed to reveal the pathological mechanisms inside the brain by profiling the tissue and bdEV proteomes in AD patients. In addition, to indicate targets for capturing and molecular profiling of bdEVs in the periphery, CNS cell-specific markers were profiled on the intact bdEV surface. METHODS bdEVs were separated and followed by EV counting and sizing. Brain tissue and bdEVs from age-matched AD patients and controls were then proteomically profiled. Total tau (t-tau), phosphorylated tau (p-tau), and antioxidant peroxiredoxins (PRDX) 1 and 6 were measured by immunoassay in an independent bdEV separation. Neuron, microglia, astrocyte, and endothelia markers were detected on intact EVs by multiplexed ELISA. RESULTS Overall, concentration of recovered bdEVs was not affected by AD. Proteome differences between AD and control were more pronounced for bdEVs than for brain tissue. Levels of t-tau, p-tau, PRDX1, and PRDX6 were significantly elevated in AD bdEVs compared with controls. Release of certain cell-specific bdEV markers was increased in AD. CONCLUSION Several bdEV proteins are involved in AD mechanisms and may be used for disease monitoring. The identified CNS cell markers may be useful tools for peripheral bdEV capture.
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Affiliation(s)
- Yiyao Huang
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tom A.P. Driedonks
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lesley Cheng
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Harinda Rajapaksha
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | | | | | - Javier Redding
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tanina Arab
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bonita H. Powell
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Pletniková
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Juan C. Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Andrew F. Hill
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
- Institute of Health and Sport, Victoria University, Melbourne, VIC, Australia
| | - Vasiliki Mahairaki
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W. Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Nagaraj R, Vaibhav V. Revising the Definition of MSMEs: Who is Likely to Benefit From it? Ind J Labour Econ 2020; 63:119-126. [PMID: 33071492 PMCID: PMC7548056 DOI: 10.1007/s41027-020-00266-x] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Raja A, Nagaraj R, Ramachandran K, Sivasubramani V, Annadurai G, Joseph Daniel D, Ramasamy P. A novel bifunctional Dy3+ activated RbCaF3 single phase phosphor: Facile synthesis and dual-luminescence properties for WLEDs and dosimetry applications. ADV POWDER TECHNOL 2020. [DOI: 10.1016/j.apt.2020.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Nagaraj R, Ramachandran K, Aravinth K, Ranjith S. Investigation on structural, optical, thermal and mechanical properties of 1, 3-dinitrobenzene (1,3-DNB) single crystal. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Nagaraj R, Stack T, Yi S, Mathew B, Shull KR, Scott EA, Mathew MT, Bijukumar DR. High Density Display of an Anti-Angiogenic Peptide on Micelle Surfaces Enhances Their Inhibition of αvβ3 Integrin-Mediated Neovascularization In Vitro. Nanomaterials (Basel) 2020; 10:E581. [PMID: 32235802 PMCID: PMC7153711 DOI: 10.3390/nano10030581] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 02/28/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Diabetic retinopathy (DR), Retinopathy of Pre-maturity (ROP), and Age-related Macular Degeneration (AMD) are multifactorial manifestations associated with abnormal growth of blood vessels in the retina. These three diseases account for 5% of the total blindness and vision impairment in the US alone. The current treatment options involve heavily invasive techniques such as frequent intravitreal administration of anti-VEGF (vascular endothelial growth factor) antibodies, which pose serious risks of endophthalmitis, retinal detachment and a multitude of adverse effects stemming from the diverse physiological processes that involve VEGF. To overcome these limitations, this current study utilizes a micellar delivery vehicle (MC) decorated with an anti-angiogenic peptide (aANGP) that inhibits αvβ3 mediated neovascularization using primary endothelial cells (HUVEC). Stable incorporation of the peptide into the micelles (aANGP-MCs) for high valency surface display was achieved with a lipidated peptide construct. After 24 h of treatment, aANGP-MCs showed significantly higher inhibition of proliferation and migration compared to free from aANGP peptide. A tube formation assay clearly demonstrated a dose-dependent angiogenic inhibitory effect of aANGP-MCs with a maximum inhibition at 4 μg/mL, a 1000-fold lower concentration than that required for free from aANGP to display a biological effect. These results demonstrate valency-dependent enhancement in the therapeutic efficacy of a bioactive peptide following conjugation to nanoparticle surfaces and present a possible treatment alternative to anti-VEGF antibody therapy with decreased side effects and more versatile options for controlled delivery.
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Affiliation(s)
- Rajini Nagaraj
- 1601 Parkveiw Ave, Regenerative Medicine and Disability Research Lab, Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA
| | - Trevor Stack
- Department of Biomedical Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Sijia Yi
- Department of Biomedical Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Benjamin Mathew
- Department of Ophthalmology and Visual Sciences, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Kenneth R Shull
- Department of Biomedical Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Evan A Scott
- Department of Biomedical Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Mathew T Mathew
- 1601 Parkveiw Ave, Regenerative Medicine and Disability Research Lab, Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA
| | - Divya Rani Bijukumar
- 1601 Parkveiw Ave, Regenerative Medicine and Disability Research Lab, Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA
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14
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Chandra D, Gayathri P, Vats M, Nagaraj R, Ray MK, Jagannadham MV. Mass spectral analysis of acetylated peptides: Implications in proteomics. Eur J Mass Spectrom (Chichester) 2020; 26:36-45. [PMID: 31234644 DOI: 10.1177/1469066719857564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sequence determination of peptides using mass spectrometry plays a crucial role in the bottom-up approaches for the identification of proteins. It is crucially important to minimise false detection and validate sequence of the peptides in order to correctly identify a protein. Chemical modification of peptides followed by mass spectrometry is an option for improving the spectral quality. In silico-derived tryptic peptides with different N-terminal amino acids were designed from human proteins and synthesized. The effect of acetylation on the fragmentation of peptides was studied. N-terminal acetylation of the tryptic peptides was shown to form b1-ions, improve the abundance and occurrence of b-ions. In some cases, the intensity and occurrence of some y-ions also varied. Thus, it is demonstrated that acetylation plays an important role in improving the de novo sequencing efficiency of the peptides. The acetylation method was extended to tryptic peptides generated from the proteome of an Antarctic bacterium Pseudomonas syringae Lz4W using the proteomics work flow and mass spectra of the peptides were analysed. Comparison of the MS/MS spectra of the acetylated and unacetylated peptides revealed that acetylation helped in improving the spectral quality and validated the peptide sequences. Using this method, 673 proteins of the 1070 proteins identified were validated.
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Affiliation(s)
- Deepika Chandra
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - P Gayathri
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Mudita Vats
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - R Nagaraj
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M K Ray
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M V Jagannadham
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
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15
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Parvathi KS, Nagalakshmi T, Mahesh C, Nagaraj R, Sunnesh A, Sameera NS, Kumar KN, Vishnubotla S. Lower limb vascular access for maintenance hemodialysis patients – A case series. J NTR Univ Health Sci 2020. [DOI: 10.4103/jdrntruhs.jdrntruhs_47_19] [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: 11/04/2022] Open
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16
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Nagaraj R, Bijukumar DR, Mathew B, Scott EA, Mathew MT. A review on recent advancements in ophthalmology devices: Currently in market and under clinical trials. J Drug Deliv Sci Technol 2019. [DOI: 10.1016/j.jddst.2019.04.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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17
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Vijayakumar R, Nagaraj R, Suthanthirakumar P, Karthikeyan P, Marimuthu K. Silver (Ag) nanoparticles enhanced luminescence properties of Dy 3+ ions in borotellurite glasses for white light applications. Spectrochim Acta A Mol Biomol Spectrosc 2018; 204:537-547. [PMID: 29975916 DOI: 10.1016/j.saa.2018.06.092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 06/25/2018] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Abstract
In the present work, the structural and optical properties of borotellurite glasses co-doped with Dy3+ ions and Ag nanoparticles were investigated. From HR-TEM analysis, the average Ag nanoparticle diameter was calculated as 13.7 ± 1 nm. The negative sign of the bonding parameter explored the ionic nature of metal-ligand (DyO) bonds. The emission spectra exhibited three emission bands in blue, yellow and red regions corresponding to 4F9/2 → 6H15/2, 4F9/2 → 6H13/2 and 4F9/2 → 6H11/2 transitions, respectively. The Yellow/Blue (Y/B) ratio of optimal BTD0.5A glass was found to be 1.881 and this low Y/B ratio indicated the fact that Dy3+ ions were located in higher symmetrical ligand environment. The CCT values are found to vary from 3717 to 3800 K and hence the present glasses may emit cool white light when excited with UV lamp. The radiative parameters were calculated for all the emission transitions by using JO theory. The decay curves are found to show non-exponential behavior for all the studied glasses. The obtained results were discussed in detail and compared with similar reported glasses.
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Affiliation(s)
- R Vijayakumar
- Key Lab of Advanced Transducers and Intelligent Control System, Ministry of Education and Shanxi Province, College of Physics and Optoelectronics, Taiyuan University of Technology, Taiyuan 030024, PR China.
| | - R Nagaraj
- SSN Research Centre, SSN College of Engineering, Kalavakkam 603 110, Tamil Nadu, India
| | - P Suthanthirakumar
- Department of Physics, Gandhigram Rural University, Gandhigram 624 302, Tamil Nadu, India
| | - P Karthikeyan
- Department of Physics, Gandhigram Rural University, Gandhigram 624 302, Tamil Nadu, India
| | - K Marimuthu
- Department of Physics, Gandhigram Rural University, Gandhigram 624 302, Tamil Nadu, India
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Yadav K, Rao JL, Srinivas R, Nagaraj R, Jagannadham MV. Characterization of acetylated histidine b 1-ion structure: A competition between oxazolone and side chain imidazole moiety. Eur J Mass Spectrom (Chichester) 2018; 24:261-268. [PMID: 29392979 DOI: 10.1177/1469066718756801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The detection of post-translational modifications of proteins is an important comprehensive research area. Over the years, proteomic studies involving protein acetylation have attracted a great deal of attention. In the present study, we have focussed on the acetylation of histidine and the intrinsic stability of b1-ion of oxazolone ring and/or with side chain imidazole bicyclic product. The formation of oxazolone structure may occur when an amino moiety undergoes acetylation reaction and when it is present in the vicinity of the side chain imidazole moiety. Tryptic peptides generated from the proteins of Acenitobacter radioresistens MMC5-containing N-terminal histidine were explored in a standard proteomic workflow. Formation of [Formula: see text] ion with an oxazolone ring in these peptides has been supported by a tandem mass spectrometric study of a synthetic peptide and density functional theory calculations. The results obtained from this study have implications in understanding the fragmentation of the peptides generated in the proteomic workflows.
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Affiliation(s)
| | - J Laxmikanth Rao
- 1 CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - R Srinivas
- 1 CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - R Nagaraj
- 2 CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M V Jagannadham
- 2 CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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Jagannadham MV, Kameshwari DB, Gayathri P, Nagaraj R. Detection of peptides with intact phosphate groups using MALDI TOF/TOF and comparison with the ESI-MS/MS. Eur J Mass Spectrom (Chichester) 2018; 24:231-242. [PMID: 29264929 DOI: 10.1177/1469066717748115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A wide variety of post-translational modifications such as oxidation, phosphorylation, glycosylation, methylation, and acetylation play critical roles in cellular functions. Detection of post-translational modifications in proteins is important to understand their crucial roles in cellular functions. Identifying each modification requires special attention in mass spectral acquisition and analysis. Here, we report a mass spectral method for the detection of multiple phosphorylations in peptides by analyzing their products after fragmentation. Synthetic peptides were used to identify these modifications by matrix-assisted laser desorption/ionization (MALDI) TOF/TOF. Peptides with serine, threonine, and tyrosine were used with mono- to tetra-phosphorylation sites in different combinations to get insights into their fragmentation and identify the location of these sites. The y-ion series were observed without the loss of phosphate groups and were thus very useful in determining the localization and sequence of the phosphate residues. Acetylation of the peptides was found to be useful in detecting the b1-ion and helped in identifying the N-terminus. When a mixture of the phosphorylated peptides (from mouse protein sequences) were analyzed by LC-MS/MS on a Velos Orbitrap Mass Spectrometer and the data subjected to analysis by Sequest using the mouse database, the peptides were identified along with the parent proteins. A comparison of MALDI TOF/TOF spectra with ESI MS/MS helped in eliminating falsely discovered peptides using the database search.
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Affiliation(s)
| | - D B Kameshwari
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - P Gayathri
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - R Nagaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
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Nagaraj R, Suthanthirakumar P, Vijayakumar R, Marimuthu K. Spectroscopic properties of Sm 3+ ions doped Alkaliborate glasses for photonics applications. Spectrochim Acta A Mol Biomol Spectrosc 2017; 185:139-148. [PMID: 28558322 DOI: 10.1016/j.saa.2017.05.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 05/03/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
A new series of Sm3+ doped alkaliborate glasses have been prepared by melt quenching technique and their structural and spectroscopic properties were analysed employing XRD, FTIR, optical absorption, photoluminescence and decay spectral measurements in order to explore their suitability for photonic applications. The amorphous nature have been confirmed through XRD analysis and the FTIR spectra reveal the presence of fundamental stretching and bending vibrations of the borate networks in the prepared glasses. From the absorption peak positions, bonding parameter (δ) values were calculated to examine the nature of the metal-ligand bond. The optical band gap (Eopt) corresponds to the direct and indirect allowed transitions and the Urbach energies (ΔE) were calculated from the absorption spectra to understand the electronic band structure of the studied glasses. The Judd-Ofelt (JO) intensity parameters Ωλ (λ=2, 4 and 6) were determined to explore the symmetry of the ligand environment around the Sm3+ ions in the studied glasses. The luminescence spectra exhibit four emission bands in the visible region due to the 4G5/2→6H5/2, 6H7/2, 6H9/2 and 6H11/2 transitions. The radiative parameters such as transition probability (A), stimulated emission cross-section (σPE), branching ratios (βR) and radiative lifetime (τR) have been determined from the luminescence spectra using JO theory to ensure the suitability of the studied glasses for optoelectronic applications. The luminescence spectra were characterized through CIE 1931 chromaticity diagram to examine the dominant emission color of the studied glasses. The lifetime values of the Sm3+ doped studied glasses pertaining to the 4G5/2 excited level have been determined through decay curve measurements and the non-exponential decay curves were fitted to the Inokuti-Hirayama model to analyze the energy transfer mechanism between the nearby Sm3+ ions. The obtained results were discussed and compared with the similar reported glasses.
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Affiliation(s)
- R Nagaraj
- Department of Physics, Gandhigram Rural University, Gandhigram, 624 302, India
| | - P Suthanthirakumar
- Department of Physics, Gandhigram Rural University, Gandhigram, 624 302, India
| | - R Vijayakumar
- Department of Physics, Sasurie College of Engineering, Vijayamangalam, 638 056, India
| | - K Marimuthu
- Department of Physics, Gandhigram Rural University, Gandhigram, 624 302, India.
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Nagaraj R, Thirugnanamurthy D, Rajput MM, Panigrahi B. Techno-economic analysis of hybrid power system sizing applied to small desalination plants for sustainable operation. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.ijsbe.2016.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Kulkarni HM, Nagaraj R, Jagannadham MV. Protective role of E. coli outer membrane vesicles against antibiotics. Microbiol Res 2015; 181:1-7. [PMID: 26640046 DOI: 10.1016/j.micres.2015.07.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [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: 03/24/2015] [Revised: 07/17/2015] [Accepted: 07/24/2015] [Indexed: 12/19/2022]
Abstract
The outer membrane vesicles (OMVs) from bacteria are known to posses both defensive and protective functions and thus participate in community related functions. In the present study, outer membrane vesicles have been shown to protect the producer bacterium and two other bacterial species from the growth inhibitory effects of some antibiotics. The OMVs isolated from E. coli MG1655 protected the bacteria against membrane-active antibiotics colistin, melittin. The OMVs of E. coli MG1655 could also protect P. aeruginosa NCTC6751 and A. radiodioresistens MMC5 against these membrane-active antibiotics. However, OMVs could not protect any of these bacteria against the other antibiotics ciprofloxacin, streptomycin and trimethoprim. Hence, OMVs appears to protect the bacterial community against membrane-active antibiotics and not other antibiotics, which have different mechanism of actions. The OMVs of E. coli MG1655 sequester the antibiotic colistin, whereas their protein components degrade the antimicrobial peptide melittin. Proteomic analysis of OMVs revealed the presence of proteases and peptidases which appear to be involved in this process. Thus, the protection of bacteria by OMVs against antibiotics is situation dependent and the mechanism differs for different situations. These studies suggest that OMVs of bacteria form a common defense for the bacterial community against specific antibiotics.
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Affiliation(s)
- Heramb M Kulkarni
- CSIR- Centre for Cellular and Molecular Biology, Tarnaka, Hyderabad 500007, India
| | - R Nagaraj
- CSIR- Centre for Cellular and Molecular Biology, Tarnaka, Hyderabad 500007, India
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Sinha K, Swamy CVB, Muralikrishna BH, Idris MM, Nagaraj R, Parnaik VK. Identification of Markers for Cellular Stress and Senescence in Laminopathic Cells by Proteomic Analysis. Proceedings of the Indian National Science Academy 2014. [DOI: 10.16943/ptinsa/2014/v80i5/47977] [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: 11/13/2022]
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Nagaraj R. Is Levinthal’s question answered after a revisit? J Biomol Struct Dyn 2013; 31:961-2. [DOI: 10.1080/07391102.2012.748528] [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: 10/27/2022]
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Varghese E, Nagaraj R, Shwethapriya R. Comparison of oral fiberoptic intubation via a modified guedel airway or a laryngeal mask airway in infants and children. J Anaesthesiol Clin Pharmacol 2013; 29:52-5. [PMID: 23493291 PMCID: PMC3590542 DOI: 10.4103/0970-9185.105797] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Though fiberoptic intubation (FOI) is considered the gold standard for securing a difficult airway in a child, it may be technically difficult in an anesthetized child. The hypothesis for this study was that it would be easier to perform FOI via a laryngeal mask airway (LMA) than a modified oropharyngeal airway with the advantage of maintaining anesthesia and oxygenation during the process. MATERIALS AND METHODS 30 children aged 6 months to 5 years undergoing elective surgery under general anesthesia were randomized to two groups to have fiberoptic bronchoscope (FOB) guided intubation either via a modified Guedel airway (FOB-ORAL) or a classic LMA (FOB-LMA). In the FOB-LMA group, the LMA was removed when a second smaller endotracheal tube was anchored to the proximal end of the tracheal tube in place. RESULTS Oral fiberoptic intubation was successful in all children. The first attempt success rate was 11/15 (73.33%) in the FOB-LMA group and 3/15 (20%) in the FOB-ORAL group (P = 0.012). Subsequent attempts at intubation were successful after 90° anticlockwise rotation of the endotracheal tube over the FOB. The time taken for fiberoptic bronchoscopy was significantly less in FOB-LMA group (59.20 ± 42.85 sec vs 108.66 ± 52.43 sec). The incidence of desaturation was higher in the FOB-ORAL group (6/15 vs 0/15). CONCLUSION In children, fiberoptic bronchoscopy and intubation via an LMA has the advantage of being easier, with shorter intubation time and continuous oxygenation and ventilation throughout the procedure. Removal of the LMA following intubation requires particular care.
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Affiliation(s)
- Elsa Varghese
- Department of Anaesthesiology, Kasturba Medical College, Manipal, Manipal University, Karnataka, India
| | - R Nagaraj
- Department of Anaesthesiology, Govt Mohan Kumaramangalam Medical College, Salem, Tamil Nadu, India
| | - R Shwethapriya
- Department of Anaesthesiology, Kasturba Medical College, Manipal, Manipal University, Karnataka, India
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Sundari CS, Chakraborty K, Nagaraj R, Jagannadham MV. Characterization of chemical modification of tryptophan by matrix-assisted laser desorption/ionization mass spectrometry. Protein Pept Lett 2010; 17:168-71. [PMID: 20214641 DOI: 10.2174/092986610790225969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tert- butylation of tryptophan (2', 5', 7'- tri tertiary butyl tryptophan), formed during acidolytic cleavage of synthetic peptides Ac-KLVYWAE-CONH(2) (A-YW) and Ac-KLVWWAE-CONH(2) (A-WW), that are analogs of the fragment of Alzheimer's beta-amyloid peptide Ac-KLVFFAE-CONH(2), during solid-phase peptide synthesis, was characterized by matrix-assisted laser desorption/ionization time of flight/time of flight (MALDI TOF/TOF) mass spectrometry. Crude peptide was fractionated by high performance liquid chromatography. Peptide fractions were sequenced and modified tryptophan was determined with the help of MALDI TOF/TOF mass spectra. Thus, it is possible to pinpoint the particular tryptophan residue that undergoes modification during synthesis of peptides containing multiple tryptophan residues.
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Affiliation(s)
- C Sivakama Sundari
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad-500 007, India
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Murugan V, Nagaraj R, Dangore A, Prabhakar S, Tewari P. Experiences with the conventional pretreatment system in the seawater reverse osmosis plant at Kalpakkam. ACTA ACUST UNITED AC 2008. [DOI: 10.1504/ijnd.2008.018927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Analysis and characterization of membrane proteins and hydrophobic peptides by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a considerable challenge because of their lower ionization efficiency. Detergents are used to solubilize hydrophobic peptides and proteins. However, in MALDI-MS, the presence of detergents can cause considerable loss of signal intensity. The extent of interference depends on the matrix/sample preparation method and experimental conditions. In the present study, we have analyzed the MALDI response of multiple fatty acylated peptides in the presence of the matrices alpha-cyano-4-hydroxy cinnamic acid (HCCA) and 2,5-dihydroxy benzoic acid (DHB). The effect of adding the nonionic detergent n-octylglucoside (OG) was also examined. The presence of OG facilitated detection of tetrapalmitoylated peptide, particularly when HCCA was used as the matrix. When DHB was used as the matrix, good signal intensity was observed in the absence of OG. Lower laser pulse rate in the linear mode of analysis resulted in good signal intensity for the tetrapalmitoylated peptide. Conditions for obtaining good signal intensities for dipalmitoylated and N-myristoyl peptides with both HCCA and DHB as matrices were also investigated.
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Affiliation(s)
- M V Jagannadham
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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Kamalakkannan S, Murugan V, Jagannadham MV, Nagaraj R, Sankaran K. Bacterial lipid modification of proteins for novel protein engineering applications. Protein Eng Des Sel 2004; 17:721-9. [PMID: 15556968 DOI: 10.1093/protein/gzh087] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Functioning of proteins efficiently at the solid-liquid interface is critical to not only biological but also modern man-made systems such as ELISA, liposomes and biosensors. Anchoring hydrophilic proteins poses a major challenge in this regard. Lipid modification, N-acyl-S-diacylglyceryl-Cys, providing an N-terminal hydrophobic membrane anchor is a viable solution that bacteria have successfully evolved but remains unexploited. Based on the current understanding of this ubiquitous and unique bacterial lipid modification it is possible to use Escherichia coli, the popular recombinant protein expression host, for converting a non-lipoprotein to a lipoprotein with a hydrophobic anchor at the N-terminal end. We report two strategies applicable to non-lipoproteins (with or without signal sequences) employing minimal sequence change. Taking periplasmic Shigella apyrase as an example, its signal sequence was engineered to include a lipobox, an essential determinant for lipid modification, or its mature sequence was fused to the signal sequence of abundant outer membrane lipoprotein, Lpp. Lipid modification was proved by membrane localization, electrophoretic mobility shift and mass spectrometric analysis. Substrate specificity and specific activity measurements indicated functional integrity after modification. In conclusion, a convenient protein engineering strategy for converting non-lipoprotein to lipoprotein for commercial application has been devised and tested successfully.
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Affiliation(s)
- S Kamalakkannan
- Centre for Biotechnology, Anna University, Chennai 600 025 and Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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Abstract
Cyclic homooligomers of mannose-derived furanoid sugar amino acid 1 [H-Maa(Bn(2))-OH] were synthesized by using BOP reagent in the presence of DIPEA under dilute conditions that converted the sugar amino acid monomer directly into its cyclic homooligomers 3a and 4a. The glucose-based sugar amino acid 2 [H-Gaa(Bn(2))-OH] under the same reaction conditions gave a bicyclic lactam 5a as the major product. Cyclic homooligomers of 2 were prepared by cyclizing their linear precursors 6 and 7 leading to the formation of cyclic peptides 8a and 9a, respectively. Conformational analysis by NMR and constrained MD studies revealed that all the cyclic products, 3, 4, 8, and 9, had symmetrical structures. The deprotected cyclic trimer of Maa 3b displayed a conformation in which all the C=O and the N-H bonds of the molecule point in opposite directions. In the deprotected cyclic tetramer of Maa 4b, the COs and NHs were in the plane of the ring with the former pointing to outside and the latter inside the ring. The structure of the cyclic Gaa dimer 8b displayed an unusual six-membered intramolecular hydrogen bond between NH(i)() --> C3-O(i)()(-)(1) and a syn orientation between the C2-H and CO. In this molecule, the C2-hydrogens and the COs can be seen on one side of the ring while the NHs point to the other side. Addition of the bicyclic lactam 5b resulted in the influx of Na(+) ions across the lipid bilayer leading to the dissipation of valinomycin-mediated K(+) diffusion potential.
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Affiliation(s)
- T K Chakraborty
- Indian Institute of Chemical Technology and Centre for Cellular and Molecular Biology, Hyderabad-500 007, India.
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Jagannadham MV, Sharadadevi A, Nagaraj R. Effects of deleting a tripeptide sequence observed in muscular dystrophy patients on the conformation of synthetic peptides corresponding to the scaffolding domain of caveolin-3. Biochem Biophys Res Commun 2002; 298:203-6. [PMID: 12387816 DOI: 10.1016/s0006-291x(02)02426-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The caveolin-scaffolding domain (CSD) is a region in caveolin-1 and 3 that mediates interactions with signaling proteins. In some patients with limb-girdle muscular dystrophy, a three amino acid micro deletion in the CSD has been observed. The conformations and aggregation behavior of synthetic peptides, corresponding to the CSD of caveolin-3: DGVWKVSYTTFTVSKYWFY and the sequence where TFT (underlined in the native sequence) has been deleted, have been investigated. Circular dichroism spectra and molecular dynamics simulations indicate distinctive differences in the conformations of the native and mutant sequences. The extent of self-association in aqueous medium is also less pronounced in the case of the peptide with the micro deletion. It is likely that the structural changes arising as a result of TFT deletion distrupt oligomerization and consequently mistargeting and degradation.
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Affiliation(s)
- M V Jagannadham
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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Abstract
Antimicrobial peptides are important components of innate immunity in species across the evolutionary scale. Unlike therapeutically used antibiotics, this class of peptides exert their activity by permeabilizing bacterial membranes. Despite the seemingly common mechanism of action, there is considerable variation in their primary structures, length and number of positive charges. Host-defense antimicrobial peptides have been the subject of extensive biophysical studies with a view at delineate structural requirements for activity. In this article, the structures of host defence antibacterial peptides and the structural requirements for activity are reviewed.
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Affiliation(s)
- N Sitaram
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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Abstract
Species across the evolutionary scale from insects to mammals deploy peptides to counter microbial invaders. Although, there are considerable differences in the primary and secondary structures of these peptides, they exert their antimicrobial activity by common mechanisms ie. by membrane permeabilization. Extensive structure-function studies have been carried out on this class of antimicrobial peptides and 'designer' peptides have been generated which possess specific antimicrobial activity. In this article the physico-chemical properties and biological activities of host-defense peptides and 'designer' peptides would be reviewed with a view to explore whether they could be used as effective therapeutic agents.
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Affiliation(s)
- N Sitaram
- Centre for Cellular and Molecular Biology, Hyderabad, India.
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Nagaraj R, Shamala N, Balaram P. Stereochemically constrained linear peptides. Conformations of peptides containing .alpha.-aminoisobutyric acid. J Am Chem Soc 2002. [DOI: 10.1021/ja00495a003] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sarma AVS, Ramana Rao MHV, Sarma JARP, Nagaraj R, Dutta AS, Kunwar AC. NMR study of cyclic peptides with renin inhibitor activity. J Biochem Biophys Methods 2002; 51:27-45. [PMID: 11879917 DOI: 10.1016/s0165-022x(01)00247-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Several cyclic analogues of renin inhibitors, based on Glu-D-Phe-Lys motif have been investigated by NMR spectroscopy and molecular dynamics calculations (MD). The 15 membered macrocycle, resulting from Glu and Lys side-chain cyclization, exhibits conformational preference. The structural evidence from NMR shows the presence of hydrogen bond between Lys NH and Glu side-chain carbonyl, resulting in a 10 membered pseudo beta-turn-like structure. The structure of the cyclic moiety is similar in all the peptides, which takes at least two conformations around Calpha-Cbeta in Glu side chain. The restrained MD calculations further support such observations and show that the macrocycle is fairly rigid, with two conformations about the Glu Calpha-Cbeta bond. The linear peptide appendages, which are essential for activity in cyclic peptides, show an extended structure in the beta-region of Ramchandran plot. These calculations also demonstrate that for the most active peptide, two major conformers each exist about the Calpha-CO bond of the Lys, D-Trp and Leu residues. In this peptide, the cyclic moiety presents a negatively charged surface formed due to the carbonyl oxygens, which are thus available to form hydrogen bonds with the receptor. The linear fragment presents further binding sites with a surface which has the hydrophobic side chains of D-Trp, Leu and D-Met on one side and carbonyls on the other side.
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Affiliation(s)
- A V S Sarma
- Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India
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Mandal M, Nagaraj R. Antibacterial activities and conformations of synthetic alpha-defensin HNP-1 and analogs with one, two and three disulfide bridges. J Pept Res 2002; 59:95-104. [PMID: 11985703 DOI: 10.1034/j.1399-3011.2002.01945.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Structure and biological activities of synthetic peptides corresponding to human alpha-defensin HNP-1, AC1YC2RIPAC3IAGERRYGTC4IYQGRLWAFC5C6 with the S-S connectivities: C1-C6, C2-C4, C3-C5, and its variants with one, two and three disulfide bridges were investigated. Oxidation of synthetic, reduced HNP-1 yielded a peptide with S-S connectivities C1-C3, C2-C4 and C5-C6, and not with the S-S linkages as in naturally occurring HNP-1. Selective protection of cysteine sulfhydryls was necessary for the formation of S-S bridges as in native HNP-1. Likewise, oxidation of peptide encompassing the segment from C2 to C5, resulted in the S-S linkages C2-C3 and C4-C5 instead of the expected linkage C2-C4 and C3-C5. Antibacterial activities were observed for all peptides, irrespective of how the S-S bridges were linked. Linear peptides without S-S bridges were inactive. Circular dichroism (CD) spectra suggest that peptides constrained by one and two S-S bridges do not form rigid beta-sheet structures in an aqueous environment. The spectrum of HNP-1 in an aqueous environment suggests the presence of a beta-hairpin conformation. In the presence of lipid vesicles, the S-S constrained peptides tend to adopt a beta-structure. Although the S-S connectivities observed in HNP-1 may be necessary for other physiological activities, such as chemotaxis, they are clearly not essential for antibacterial activity.
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Affiliation(s)
- M Mandal
- Centre for Cellular and Molecular Biology, Hyderabad, India
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Mandal M, Jagannadham MV, Nagaraj R. Antibacterial activities and conformations of bovine beta-defensin BNBD-12 and analogs:structural and disulfide bridge requirements for activity. Peptides 2002; 23:413-8. [PMID: 11835989 DOI: 10.1016/s0196-9781(01)00628-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Structure and biological activities of synthetic peptides corresponding to bovine neutrophil beta-defensin BNBD-12, GPLSC(1)GRNGGVC(2)IPIRC(3) PVPMRQIGTC(4) FGRPVKC(5) C(6)RSW with disulfide connectivities C(1)-C(5), C(2)-C(4) and C(3)-C(6) and its variants with one, two and three disulfide bridges have been investigated. Selective protection of cysteine thiols was necessary in the four and six cysteine containing peptides for the formation of disulfide connectivities as observed in BNBD-12. Circular dichroism (CD) spectra indicate that in aqueous medium, only a small fraction of molecules populate turn-like conformations. In the presence of micelles and lipid vesicles, the single, two and three disulfide containing peptides adopt beta-hairpin or beta-sheet structures. Antibacterial activity was observed for all the peptides, irrespective of the number of disulfide bridges or how they were connected. Our results suggest that a rigid beta-sheet structure or the presence of three disulfide bridges does not appear to be stringent requirements for antibacterial activity in beta-defensins.
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Affiliation(s)
- M Mandal
- Centre for Cellular and Molecular Biology, Uppal Road, 500 007, Hyderabad, India
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Moudgal NR, Krishnamurthy HN, Surekha S, Krishnamurthy H, Dhople VM, Nagaraj R, Sairam MR. Immunobiology of a synthetic luteinizing hormone receptor peptide 21-41. J Androl 2001; 22:992-8. [PMID: 11700864 DOI: 10.1002/j.1939-4640.2001.tb03440.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Immunization of adult male rabbits with a synthetic luteinizing hormone-receptor peptide (LH-RP; representing amino-acids 21-41 of the extracellular domain of the rat LH receptor) resulted in production of high-titer antibodies capable of interacting with particulate and cell-based LH receptors. The antibody produced was able to inhibit binding of 125I-labeled human chorionic gonadotropin (hCG) to a particulate sheep luteal LH receptor preparation by 40%-50%. Maximal inhibitory activity was correlated with high antibody titer. Immunocytometry revealed that the antibody could directly bind to cells having LH receptors, such as rat granulosa and Leydig cells. The antibodies recognized a 77-kilodalton membrane protein in Western blots of mouse testicular extracts. Interaction of endogenous Leydig cell LH receptor with the LH-RP antibody resulted in both hormone agonist and antagonistic activities. The hormone-mimicking activity (increase in serum testosterone over control) was confined only to the early phase of immunization when the antibody titer was low. Blockade of LH receptor during the later part of immunization resulted in a significant reduction in serum testosterone over controls and inhibition of spermatogenesis. DNA flow cytometry showed that a specific and significant inhibition of meiosis (transformation of primary spermatocytes to round and elongated spermatids P < .01) and spermiogenesis (transformation of round spermatids to elongated spermatids P < .0001) occurred following blockade of LH function.
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Affiliation(s)
- N R Moudgal
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore
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41
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Kumari VK, Nagaraj R. Structure-function studies on the amphibian peptide brevinin 1E: translocating the cationic segment from the C-terminal end to a central position favors selective antibacterial activity. J Pept Res 2001; 58:433-41. [PMID: 11892852 DOI: 10.1034/j.1399-3011.2001.00924.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Brevinin 1E, which has the sequence FLPLLAGLAANFLPKIFCKITRKC, is an antimicrobial peptide isolated from the skin secretions of the European frog Rana esculenta. Both the linear and the disulfide-bridged forms have relatively broad-spectrum antibacterial as well as hemolytic activities. The antibacterial and hemolytic activities and biophysical properties of synthetic peptides corresponding to brevinin 1E and its analog in which the segment CKITRKC has been transposed to a central location resulting in the sequence FLPLLAGLCKITRKCAANFLPKIF have been investigated. Our studies indicate that the analog peptide has antibacterial activity comparable with brevinin 1E, but with considerably reduced hemolytic activity. The linear variant of the analog has no hemolytic activity, unlike the linear form of brevinin 1E. The biological activities can be explained on the basis of relative affinities for anionic and zwitterionic lipids. A cluster of cationic amino acids flanked on one side by a hydrophobic stretch of amino acids and another side composed of apolar amino acids appears to favor preferential antibacterial activity.
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Affiliation(s)
- V K Kumari
- Center for Cellular and Molecular Biology, Hyderabad, India
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42
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Thennarasu S, Nagaraj R. Effects of salt and denaturant on structure of the amino terminal alpha-helical segment of an antibacterial peptide dermaseptin and its binding to model membranes. INDIAN JOURNAL OF BIOCHEMISTRY & BIOPHYSICS 2001; 38:142-8. [PMID: 11693375] [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] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The amino terminal 1-18 domain of dermaseptin s is an important determinant of its structure as well as the antibacterial activity. A thorough investigation on the structure of the 18-residue peptide (D18) and its binding to model membranes in presence of salt and denaturant guanidinium chloride has been carried out. In presence of salt, there is an increase in the fraction of peptide molecules in helical conformation. In presence of the denaturant, D18 is unordered, but addition of the structure-promoting solvent trifluoroethanol results in a transition to the helical conformation. In presence of denaturant, the peptide is unordered, but binding to lipid vesicles is not abolished. Investigation of model membrane permeabilizing ability of the peptide in solutions containing various proportions of sodium chloride and guanidinium chloride indicates that vesicle permeabilization parallels extent of binding. The peptide thus binds to lipid vesicles in an unfolded state. Since the peptide has propensity to fold into a helical conformation, lipid induced transition to a helical structure occurs, followed by membrane permeabilization as a result of pore formation.
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Affiliation(s)
- S Thennarasu
- Centre for Cellular and Molecular Biology, Hyderabad, India
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43
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Sai KP, Jagannadham MV, Vairamani M, Raju NP, Devi AS, Nagaraj R, Sitaram N. Tigerinins: novel antimicrobial peptides from the Indian frog Rana tigerina. J Biol Chem 2001; 276:2701-7. [PMID: 11031261 DOI: 10.1074/jbc.m006615200] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Four broad-spectrum, 11 and 12 residue, novel antimicrobial peptides have been isolated from the adrenaline-stimulated skin secretions of the Indian frog Rana tigerina. Sequences of these peptides have been determined by automated Edman degradation, by mass spectral analysis and confirmed by chemical synthesis. These peptides, which we have named as tigerinins, are characterized by an intramolecular disulfide bridge between two cysteine residues forming a nonapeptide ring. This feature is not found in other amphibian peptides. Conformational analysis indicate that the peptides tend to form beta-turn structures. The peptides are cationic and exert their activity by permeabilizing bacterial membranes. Tigerinins represent the smallest, nonhelical, cationic antimicrobial peptides from amphibians.
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Affiliation(s)
- K P Sai
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
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44
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Subbalakshmi C, Nagaraj R, Sitaram N. Biological activities of retro and diastereo analogs of a 13-residue peptide with antimicrobial and hemolytic activities. J Pept Res 2001; 57:59-67. [PMID: 11168889 DOI: 10.1034/j.1399-3011.2001.00800.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The biological activities of synthetic retro and diastereo analogs of PKLLKTFLSKWIG (SPFK), a 13-residue peptide with antimicrobial and hemolytic activities, have been investigated. Retro peptides with C-terminal acid and amide exhibited antibacterial activities comparable with those of SPFK. Their hemolytic activities were, however, only marginally lower. The diastereo analog with C-terminal acid was not antibacterial and was weakly hemolytic. Amidation of this analog could restore antibacterial activity. Both retro analogs were unordered in aqueous medium but had a propensity for a helical structure in trifluoroethanol. However, diastereo analogs were unordered in both aqueous medium and trifluoroethanol. Thus, reversing the sequence in a short amphiphilic peptide may not always result in the selective loss of biological activity such as hemolytic activity. Also, introduction of enantiomeric amino acids in a short peptide to generate a diastereomer may result in loss of structure as well as antimicrobial and hemolytic activities, unless compensated by an increase in positive charges.
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Affiliation(s)
- C Subbalakshmi
- Centre for Cellular and Molecular Biology, Hyderabad, India
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45
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Chakraborty TK, Ghosh S, Jayaprakash S, Sarma JA, Ravikanth V, Diwan PV, Nagaraj R, Kunwar AC, Sharma JA. Synthesis and conformational studies of peptidomimetics containing furanoid sugar amino acids and a sugar diacid. J Org Chem 2000; 65:6441-57. [PMID: 11052087 DOI: 10.1021/jo000408e] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Furanoid sugar amino acids (1) were synthesized and used as dipeptide isosteres to induce interesting turn structures in small linear peptides. They belong to a new variety of designed hybrid structures that carry both amino and carboxyl groups on rigid furanose sugar rings. Four such molecules, 6-amino-2,5-anhydro-6-deoxy-D-gluconic acid (3, Gaa) and its mannonic (4, Maa), idonic (5, Iaa), and a 3,4-dideoxyidonic (6, ddIaa) congeners were synthesized. The synthesis followed a novel reaction path in which an intramolecular 5-exo S(N)2 opening of the hexose-derived terminal aziridine ring in 2 by the gamma-benzyloxy oxygen with concomitant debenzylation occurred during pyridinium dichromate oxidation of the primary delta-hydroxyl group to carboxyl function, leading to the formation of furanoid sugar amino acid frameworks in a single step. Incorporation of these furanoid sugar amino acids into Leu-enkephalin replacing its Gly-Gly portion gave analogues 8-11. Detailed structural analysis of these molecules by circular dichroism (CD) and various NMR techniques in combination with constrained molecular dynamics (MD) simulations revealed that two of these analogues, 8a and 10a, have folded conformations composed of an unusual nine-membered pseudo beta-turn-like structure with a strong intramolecular H-bond between LeuNH --> sugarC3-OH. This, in turn, brings the two aromatic rings of Tyr and Phe in close proximity, a prerequisite for biological activities of opioid peptides. The analgesic activities of 8a,b determined by mouse hot-plate and tail-clip methods were similar to that of Leu-enkephalin methyl ester. The syn disposition of the beta-hydroxycarboxyl motif on the sugar rings appears to be the driving force to nucleate the observed turn structures in some of these molecules (8 and 10). Repetition of the motif on both sides of a furanose ring resulted in a novel molecular design of sugar diacid, 2,5-anhydro-D-idaric acid (7, Idac). Bidirectional elongation of the diacid moieties of 7 with identical peptide strands led to the formation of a C2-symmetric reverse-turn mimetic 12 which displayed a very ordered structure consisting of identical intramolecular H-bonds at two ends between LeuNH --> sugar-OH, the same as in 8 and 10.
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Affiliation(s)
- T K Chakraborty
- Indian Institute of Chemical Technology and Centre for Cellular and Molecular Biology, Hyderabad, India.
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46
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Abstract
How multifunctional signals combine to specify unique cell fates during pattern formation is not well understood. Here, we demonstrate that together with the transcription factor Lozenge, the nuclear effectors of the EGFR and Notch signaling pathways directly regulate D-Pax2 transcription in cone cells of the Drosophila eye disc. Moreover, the specificity of D-Pax2 expression can be altered upon genetic manipulation of these inputs. Thus, a relatively small number of temporally and spatially controlled signals received by a set of pluripotent cells can create the unique combinations of activated transcription factors required to regulate target genes and ultimately specify distinct cell fates within this group. We expect that similar mechanisms may specify pattern formation in vertebrate developmental systems that involve intercellular communication.
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Affiliation(s)
- G V Flores
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California at Los Angeles 90095, USA
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Subbalakshmi C, Bikshapathy E, Sitaram N, Nagaraj R. Antibacterial and hemolytic activities of single tryptophan analogs of indolicidin. Biochem Biophys Res Commun 2000; 274:714-6. [PMID: 10924341 DOI: 10.1006/bbrc.2000.3214] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure and biological activities of analogs of the bovine neutrophil antibacterial and hemolytic peptide indolicidin, ILPWKWPWWPWRR-amide, where one tryptophan at 4th, 8th, or 11th position has been retained and the others replaced by leucine, have been investigated. All the single tryptophan analogs exhibit antibacterial activity. However, unlike indolicidin, they do not lyse erythrocytes. Structure analysis by circular dichroism spectroscopy indicates that the analogs are unordered in aqueous medium and adopt beta-turn structures in trifluoroethanol and micelles. The tryptophan residues in indolicidin appear to be essential for hemolytic activity but not antibacterial activity. The nonspecific biological activities of indolicidin and specific antibacterial activity of single tryptophan analogs suggest that in short peptides, a motif composed of hydrophobic amino acids with the exception of tryptophan, interspaced with proline residues and cationic amino acids at the N or C termini would favor selective antibacterial activity.
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Affiliation(s)
- C Subbalakshmi
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
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48
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Ranganathan D, Haridas V, Nagaraj R, Karle IL. Double-helical cyclic peptides: design, synthesis, and crystal structure of figure-eight mirror-image conformers of adamantane-constrained cystine-containing cyclic peptide cyclo (Adm-Cyst)(3). J Org Chem 2000; 65:4415-22. [PMID: 10891146 DOI: 10.1021/jo0003807] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A large number of macrocycles containing alternating repeats of cystine diOMe(-NH-CH(CO(2)Me)-CH(2)-S-)(2) and either a conformationally rigid aromatic/alicyclic moiety or a flexible polymethylene unit (X) in the cyclic backbone with ring size varying from 13- to 78-membered have been examined by spectral ((1)H NMR, FT-IR, CD) and X-ray crystallography studies for unusual conformational preferences. While (1)H NMR measurements indicated a turnlike conformation for all macrocycles, stabilized by intramolecular NH.CO hydrogen bonding, as also supported by FT-IR spectra in chloroform, convincing proof for beta-turn structures was provided by circular dichroism studies. Single-crystal X-ray studies on 39-membered cyclo (Adm-L-Cyst)(3) revealed a double-helical fold (figure-eight motif) for the macrocycle. Only a right-handed double helix was seen in the macrocycle constructed from L-cystine. The mirror-image macrocycle made up of D-cystine units exhibited a double helix with exactly the opposite screw sense, as expected. The enantiomeric figure-eights were stabilized by two intramolecular NH. CO hydrogen bonds and exhibited identical (1) H NMR and FT-IR spectra. The CD spectra of both isomers had a mirror-image relationship. The present results have clearly brought out the importance of cystine residues in inducing turn conformation that may be an important deciding factor for the adoption of topologically important structures by macrocycles containing multiple S-S linkages.
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Affiliation(s)
- D Ranganathan
- Discovery Laboratory, Indian Institute of Chemical Technology, Hyderabad, India.
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49
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Arunan C, Nagaraj R, Rajasekharan Pillai VN. Solid-phase synthesis of a modified 13-residue seminalplasmin fragment on 1,6-hexanediol diacrylate-crosslinked polystyrene support. Peptides 2000; 21:773-7. [PMID: 10958996 DOI: 10.1016/s0196-9781(00)00207-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A novel 1,6-hexanediol diacrylate cross-linked resin was prepared that was subsequently functionalized by using chloromethyl methyl ether to afford a high-capacity resin. The resin exhibited good swelling and its application in the successful synthesis of a 13-residue peptide corresponding to the fragment of seminalplasmin has been illustrated. The resin was chemically inert at peptide synthetic conditions.
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Affiliation(s)
- C Arunan
- School of Chemical Sciences, Mahatma Gandhi University, Kottayam, 686560, Kerala, India.
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50
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Ranganathan D, Haridas V, Kurur S, Nagaraj R, Bikshapathy E, Kunwar AC, Sarma AV, Vairamani M. Norbornene-constrained cyclic peptides with hairpin architecture: design, synthesis, conformation, and membrane ion transport. J Org Chem 2000; 65:365-74. [PMID: 10813943 DOI: 10.1021/jo9912045] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel family of hairpin cyclic peptides has been designed on the basis of the use of norbornene units as the bridging ligands. The design is flexible with respect to the choice of an amino acid, the ring size, and the nature of the second bridging ligand as illustrated here with the preparation of a large number of norborneno cyclic peptides containing a variety of amino acids in ring sizes varying from 12- to 29-membered, with the choice of the second bridging ligand being a rigid norbornene (11, 13a,b), an adamantane unit (7a,b and 8), or a flexible cystine residue (4a,b and 10). The presence of built-in handles (as protected COOH groups) permits the attachment of a variety of subunits as shown here with the ligation of Leu-Leu, Val-Val, or Aib-Aib pendants in 4b, 7b, and 13b, respectively. This novel class of constrained cyclic peptides are demonstrated to adopt beta-sheet- or hairpin-like conformation as shown by (1)H NMR and CD spectra. Membrane ion-transport studies have shown that the norborneno cyclic peptides 4b and 7b containing Leu-Leu or Val-Val pendants symmetrically placed on the exterior of the ring show high efficiency and selectivity in the transport of specifically monovalent cations. This property can be attributed to the hairpin-like architecture induced by the norbornene unit since the bis-adamantano peptide 15 containing two pairs of Leu-Leu pendants on the exterior is able to transport both monovalent (Na(+), K(+)) and divalent (Mg(2+)/Ca(2+)) cations.
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Affiliation(s)
- D Ranganathan
- Discovery Laboratory, Indian Institute of Chemical Technology, and Centre for Cellular and Molecular Biology, Hyderabad-500 007, India.
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