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Article ; Online: Bisbenzylisoquinolines from Cissampelos pareira L. as antimalarial agents: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies.

Suresh, Patil Shivprasad / Kesarwani, Veerbhan / Kumari, Surekha / Shankar, Ravi / Sharma, Upendra

Computational biology and chemistry

2023 Volume 104, Page(s) 107826

Abstract: Malaria is a major global health issue due to the emergence of resistance to most of the available antimalarial drugs. There is an urgent need to discover new antimalarials to tackle the resistance issue. The present study aims to explore the ... ...

Abstract	Malaria is a major global health issue due to the emergence of resistance to most of the available antimalarial drugs. There is an urgent need to discover new antimalarials to tackle the resistance issue. The present study aims to explore the antimalarial potential of chemical constituents reported from Cissampelos pareira L., a medicinal plant traditionally known for treating malaria. Phytochemically, benzylisoquinolines and bisbenzylisoquinolines are the major classes of alkaloids reported from this plant. In silico molecular docking revealed prominent interactions of bisbenzylisoquinolines such as hayatinine and curine with Pfdihydrofolate reductase (-6.983 Kcal/mol and -6.237 Kcal/mol), PfcGMP-dependent protein kinase (-6.652 Kcal/mol and -7.158 Kcal/mol), and Pfprolyl-tRNA synthetase (-7.569 Kcal/mol and -7.122 Kcal/mol). The binding affinity of hayatinine and curine with identified antimalarial targets was further evaluated using MD-simulation analysis. Among the identified antimalarial targets, the RMSD, RMSF, the radius of gyration, and PCA indicated the formation of stable complexes of hayatinine and curine with Pfprolyl-tRNA synthetase. The outcomes of in silico investigation putatively suggested that bisbenzylisoquinolines may act on the translation of the Plasmodium parasite to exhibit antimalarial potency.
MeSH term(s)	Humans ; Antimalarials/pharmacology ; Antimalarials/chemistry ; Benzylisoquinolines ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Cissampelos/chemistry ; Plants, Medicinal ; Malaria/drug therapy ; Amino Acyl-tRNA Synthetases
Chemical Substances	Antimalarials ; Benzylisoquinolines ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-)
Language	English
Publishing date	2023-02-12
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2023.107826
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Corrigendum to "Self-assembled chitosan polymer intercalating peptide functionalized gold nanoparticles as nanoprobe for efficient imaging of urokinase plasminogen activator receptor in cancer diagnostics" [Carbohydrate Polymers, 266, (2021) 118138].

Shahdeo, Deepshikha / Kesarwani, Veerbhan / Suhag, Deepa / Ahmed, Jahangeer / Alshehri, Saad M / Gandhi, Sonu

Carbohydrate polymers

2022 Volume 284, Page(s) 119239

Language	English
Publishing date	2022-02-12
Publishing country	England
Document type	Published Erratum
ZDB-ID	1501516-6
ISSN	1879-1344 ; 0144-8617
ISSN (online)	1879-1344
ISSN	0144-8617
DOI	10.1016/j.carbpol.2022.119239
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Electroactive reduced graphene oxide for highly sensitive detection of secretory non-structural 1 protein: A potential diagnostic biomarker for Japanese encephalitis virus

Roberts, Akanksha / Kesarwani, Veerbhan / Gupta, Rupal / Gandhi, Sonu

Biosensors & bioelectronics. 2022 Feb. 15, v. 198

2022

Abstract: Fluorine Doped Tin Oxide (FTO) electrode was fabricated with reduced Graphene Oxide (rGO) for sensitive detection of Japanese encephalitis virus (JEV) non-structural 1 (NS1) protein. Beforehand, in-silico 3D structure, stability, and docking of ... ...

Abstract	Fluorine Doped Tin Oxide (FTO) electrode was fabricated with reduced Graphene Oxide (rGO) for sensitive detection of Japanese encephalitis virus (JEV) non-structural 1 (NS1) protein. Beforehand, in-silico 3D structure, stability, and docking of recombinant JEV NS1 antigen (NS1–Ag) and antibody (Ab) was evaluated. The recombinant NS1 Ag of 42 kDa was produced in-house by successful cloning into pET-28a(+) plasmid and further expressed using BL21 Escherichia coli (E. coli) cells. The NS1 Ag was used to raise polyclonal antibodies (Ab) and both were characterized via Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE), Western Blot, Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF), and Enzyme-Linked Immunosorbent Assay (ELISA). Further characterisation of all binding events such as rGO synthesis, and its conjugation with NS1 Ab, and NS1 Ag were confirmed through Fourier-Transform Infrared Spectroscopy (FTIR), Raman Spectroscopy, Energy Dispersive X-Ray Analysis (EDX), Scanning Electron Microscopy (SEM), Cyclic Voltammetry (CV) and Differential Pulse Voltammetry (DPV). The fabricated FTO electrode was optimised for various parameters such as pH, response time, temperature, concentration, and scan rate. The detection of JEV NS1 Ag was performed in buffer (LOD- 0.92 fM) as well in spiked serum (LOD- 1.3 fM) samples. The JEV NS1 Ab showed negligible cross-reactivity with other flaviviral NS1 Ag, provided a rapid response within 5 s, and remained stable up to 4 weeks. Furthermore, the fabricated immunosensor may be a potential candidate for further miniaturisation for accurate and early diagnosis of JEV in clinical samples.
Keywords	Escherichia coli ; Fourier transform infrared spectroscopy ; Japanese encephalitis virus ; Raman spectroscopy ; Western blotting ; antigens ; biomarkers ; blood serum ; computer simulation ; cross reaction ; early diagnosis ; electrodes ; energy-dispersive X-ray analysis ; enzyme-linked immunosorbent assay ; fluorine ; graphene oxide ; immunosensors ; pH ; plasmids ; polyacrylamide gel electrophoresis ; sodium dodecyl sulfate ; temperature ; tin dioxide ; voltammetry
Language	English
Dates of publication	2022-0215
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1011023-9
ISSN	1873-4235 ; 0956-5663
ISSN (online)	1873-4235
ISSN	0956-5663
DOI	10.1016/j.bios.2021.113837
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Electroactive reduced graphene oxide for highly sensitive detection of secretory non-structural 1 protein: A potential diagnostic biomarker for Japanese encephalitis virus.

Roberts, Akanksha / Kesarwani, Veerbhan / Gupta, Rupal / Gandhi, Sonu

Biosensors & bioelectronics

2021 Volume 198, Page(s) 113837

Abstract	Fluorine Doped Tin Oxide (FTO) electrode was fabricated with reduced Graphene Oxide (rGO) for sensitive detection of Japanese encephalitis virus (JEV) non-structural 1 (NS1) protein. Beforehand, in-silico 3D structure, stability, and docking of recombinant JEV NS1 antigen (NS1-Ag) and antibody (Ab) was evaluated. The recombinant NS1 Ag of 42 kDa was produced in-house by successful cloning into pET-28a(+) plasmid and further expressed using BL21 Escherichia coli (E. coli) cells. The NS1 Ag was used to raise polyclonal antibodies (Ab) and both were characterized via Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE), Western Blot, Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF), and Enzyme-Linked Immunosorbent Assay (ELISA). Further characterisation of all binding events such as rGO synthesis, and its conjugation with NS1 Ab, and NS1 Ag were confirmed through Fourier-Transform Infrared Spectroscopy (FTIR), Raman Spectroscopy, Energy Dispersive X-Ray Analysis (EDX), Scanning Electron Microscopy (SEM), Cyclic Voltammetry (CV) and Differential Pulse Voltammetry (DPV). The fabricated FTO electrode was optimised for various parameters such as pH, response time, temperature, concentration, and scan rate. The detection of JEV NS1 Ag was performed in buffer (LOD- 0.92 fM) as well in spiked serum (LOD- 1.3 fM) samples. The JEV NS1 Ab showed negligible cross-reactivity with other flaviviral NS1 Ag, provided a rapid response within 5 s, and remained stable up to 4 weeks. Furthermore, the fabricated immunosensor may be a potential candidate for further miniaturisation for accurate and early diagnosis of JEV in clinical samples.
MeSH term(s)	Antibodies, Viral ; Biomarkers ; Biosensing Techniques ; Encephalitis Virus, Japanese ; Escherichia coli/genetics ; Graphite ; Immunoassay ; Viral Nonstructural Proteins/genetics
Chemical Substances	Antibodies, Viral ; Biomarkers ; Viral Nonstructural Proteins ; graphene oxide ; Graphite (7782-42-5)
Language	English
Publishing date	2021-11-29
Publishing country	England
Document type	Journal Article
ZDB-ID	1011023-9
ISSN	1873-4235 ; 0956-5663
ISSN (online)	1873-4235
ISSN	0956-5663
DOI	10.1016/j.bios.2021.113837
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Non-Synonymous Variants in Fat QTL Genes among High- and Low-Milk-Yielding Indigenous Breeds.

Topno, Neelam A / Kesarwani, Veerbhan / Kushwaha, Sandeep Kumar / Azam, Sarwar / Kadivella, Mohammad / Gandham, Ravi Kumar / Majumdar, Subeer S

Animals : an open access journal from MDPI

2023 Volume 13, Issue 5

Abstract: The effect of breed on milk components-fat, protein, lactose, and water-has been observed to be significant. As fat is one of the major price-determining factors for milk, exploring the variations in fat QTLs across breeds would shed light on the ... ...

Abstract	The effect of breed on milk components-fat, protein, lactose, and water-has been observed to be significant. As fat is one of the major price-determining factors for milk, exploring the variations in fat QTLs across breeds would shed light on the variable fat content in their milk. Here, on whole-genome sequencing, 25 differentially expressed hub or bottleneck fat QTLs were explored for variations across indigenous breeds. Out of these, 20 genes were identified as having nonsynonymous substitutions. A fixed SNP pattern in high-milk-yielding breeds in comparison to low-milk-yielding breeds was identified in the genes
Language	English
Publishing date	2023-02-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606558-7
ISSN	2076-2615
ISSN	2076-2615
DOI	10.3390/ani13050884
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Article ; Online: Polymeric biocompatible iron oxide nanoparticles labeled with peptides for imaging in ovarian cancer.

Shahdeo, Deepshikha / Roberts, Akanksha / Kesarwani, Veerbhan / Horvat, Milena / Chouhan, Raghuraj Singh / Gandhi, Sonu

Bioscience reports

2022 Volume 42, Issue 2

Abstract: Compared with other nanomaterials, surface-modified iron oxide nanoparticles (IONPs) have gained attraction for cancer therapy applications due to its low toxicity, and long retention time. An innocuous targeting strategy was developed by generation of ... ...

Abstract	Compared with other nanomaterials, surface-modified iron oxide nanoparticles (IONPs) have gained attraction for cancer therapy applications due to its low toxicity, and long retention time. An innocuous targeting strategy was developed by generation of fluorescein isothiocyanate (FITC)-labeled peptide (growth factor domain (GFD) and somatomedin B domain (SMB)) functionalized, chitosan-coated IONPs (IONPs/C). It can be used to target urokinase plasminogen activator receptor (uPAR), which is a surface biomarker, in ovarian cancer. Binding affinity between uPAR and peptides (GFD and SMB) were revealed by in-silico docking studies. The biophysical characterizations of IONPs, IONPs/C, and IONPs/C/GFD-FITC or SMB-FITC nanoprobes were assessed via Vibrating Sample Magnetometer (VSM), Transmission Electron Microscopy (TEM), Dynamic Light Scattering (DLS), and Fourier Transform Infrared Spectroscopy (FT-IR). Prussian Blue staining, fluorescence spectroscopy, and fluorescence imaging were performed to confirm the targeting of nanoprobes with the surface receptor uPAR. The combination of IONPs/C/GFD+SMB showed efficient targeting of uPAR in the tumor microenvironment, and thus can be implemented as a molecular magnetic nanoprobe for cancer cell imaging and targeting.
MeSH term(s)	Chitosan/chemistry ; Humans ; Magnetic Iron Oxide Nanoparticles ; Ovarian Neoplasms/diagnostic imaging ; Peptides/chemistry ; Spectroscopy, Fourier Transform Infrared ; Tumor Microenvironment
Chemical Substances	Peptides ; Chitosan (9012-76-4)
Language	English
Publishing date	2022-02-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	764946-0
ISSN	1573-4935 ; 0144-8463
ISSN (online)	1573-4935
ISSN	0144-8463
DOI	10.1042/BSR20212622
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Article ; Online: Non-Synonymous Variants in Fat QTL Genes among High- and Low-Milk-Yielding Indigenous Breeds

Neelam A. Topno / Veerbhan Kesarwani / Sandeep Kumar Kushwaha / Sarwar Azam / Mohammad Kadivella / Ravi Kumar Gandham / Subeer S. Majumdar

Animals, Vol 13, Iss 884, p

2023 Volume 884

Abstract: The effect of breed on milk components—fat, protein, lactose, and water—has been observed to be significant. As fat is one of the major price-determining factors for milk, exploring the variations in fat QTLs across breeds would shed light on the ... ...

Abstract	The effect of breed on milk components—fat, protein, lactose, and water—has been observed to be significant. As fat is one of the major price-determining factors for milk, exploring the variations in fat QTLs across breeds would shed light on the variable fat content in their milk. Here, on whole-genome sequencing, 25 differentially expressed hub or bottleneck fat QTLs were explored for variations across indigenous breeds. Out of these, 20 genes were identified as having nonsynonymous substitutions. A fixed SNP pattern in high-milk-yielding breeds in comparison to low-milk-yielding breeds was identified in the genes GHR, TLR4, LPIN1, CACNA1C, ZBTB16, ITGA1, ANK1, and NTG5E and, vice versa, in the genes MFGE8, FGF2, TLR4, LPIN1, NUP98, PTK2, ZTB16, DDIT3 , and NT5E . The identified SNPs were ratified by pyrosequencing to prove that key differences exist in fat QTLs between the high- and low-milk-yielding breeds.
Keywords	milk fat ; whole-genome sequencing ; SNPs ; genomic variation ; variant calling ; indigenous breeds ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Subject code	630
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Non-Synonymous Variants in Fat QTL Genes among High- and Low-Milk-Yielding Indigenous Breeds

Topno, Neelam A. / Kesarwani, Veerbhan / Kushwaha, Sandeep Kumar / Azam, Sarwar / Kadivella, Mohammad / Gandham, Ravi Kumar / Majumdar, Subeer S.

Animals. 2023 Feb. 28, v. 13, no. 5

2023

Abstract	The effect of breed on milk components—fat, protein, lactose, and water—has been observed to be significant. As fat is one of the major price-determining factors for milk, exploring the variations in fat QTLs across breeds would shed light on the variable fat content in their milk. Here, on whole-genome sequencing, 25 differentially expressed hub or bottleneck fat QTLs were explored for variations across indigenous breeds. Out of these, 20 genes were identified as having nonsynonymous substitutions. A fixed SNP pattern in high-milk-yielding breeds in comparison to low-milk-yielding breeds was identified in the genes GHR, TLR4, LPIN1, CACNA1C, ZBTB16, ITGA1, ANK1, and NTG5E and, vice versa, in the genes MFGE8, FGF2, TLR4, LPIN1, NUP98, PTK2, ZTB16, DDIT3, and NT5E. The identified SNPs were ratified by pyrosequencing to prove that key differences exist in fat QTLs between the high- and low-milk-yielding breeds.
Keywords	gene expression regulation ; high-throughput nucleotide sequencing ; lactose ; lipid content ; milk
Language	English
Dates of publication	2023-0228
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2606558-7
ISSN	2076-2615
ISSN	2076-2615
DOI	10.3390/ani13050884
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Self-assembled chitosan polymer intercalating peptide functionalized gold nanoparticles as nanoprobe for efficient imaging of urokinase plasminogen activator receptor in cancer diagnostics.

Shahdeo, Deepshikha / Kesarwani, Veerbhan / Suhag, Deepa / Ahmed, Jahangeer / Alshehri, Saad M / Gandhi, Sonu

Carbohydrate polymers

2021 Volume 266, Page(s) 118138

Abstract: Targeting cell surface receptors for specific drug delivery in cancer has garnered lot of attention. Urokinase plasminogen activator receptor (uPAR), a surface biomarker, is overexpressed on many tumours including breast, colorectal, prostate, and ... ...

Abstract	Targeting cell surface receptors for specific drug delivery in cancer has garnered lot of attention. Urokinase plasminogen activator receptor (uPAR), a surface biomarker, is overexpressed on many tumours including breast, colorectal, prostate, and ovarian cancers. Binding of growth factor domain (GFD) of urokinase plasminogen activator (uPA) with uPAR lead to its close conformation, and allow somatomedin B domain (SMB) of vitronectin binding by allosteric modulation. In-silico docking of uPAR with GFD and SMB peptides was performed to identify potential binding affinity. Herein, we report fluorescently labeled peptide functionalized AuNPs with a mixed self-assembled monolayer of intercalating chitosan polymer for efficient targeting and imaging of uPAR-positive cells. The biophysical characterization of nanoconjugates and uPAR-specific targeting was assessed by FACS, cell adhesion, and fluorescence imaging. AuNPs/chitosan/GFD+SMB peptides showed higher uptake as compared to AuNPs/chitosan/GFD, and AuNPs/chitosan/SMB that can be utilized as a tool for molecular targeting and imaging in metastasis.
MeSH term(s)	Cell Line, Tumor ; Chitosan/chemistry ; Chitosan/toxicity ; Gold/chemistry ; Gold/toxicity ; Humans ; Immobilized Proteins/chemistry ; Immobilized Proteins/metabolism ; Immobilized Proteins/toxicity ; Metal Nanoparticles/chemistry ; Metal Nanoparticles/toxicity ; Microscopy, Fluorescence ; Molecular Docking Simulation ; Neoplasms/diagnostic imaging ; Neoplasms/metabolism ; Peptides/chemistry ; Peptides/metabolism ; Peptides/toxicity ; Protein Binding ; Receptors, Urokinase Plasminogen Activator/metabolism
Chemical Substances	Immobilized Proteins ; PLAUR protein, human ; Peptides ; Receptors, Urokinase Plasminogen Activator ; Gold (7440-57-5) ; Chitosan (9012-76-4)
Language	English
Publishing date	2021-04-30
Publishing country	England
Document type	Journal Article
ZDB-ID	1501516-6
ISSN	1879-1344 ; 0144-8617
ISSN (online)	1879-1344
ISSN	0144-8617
DOI	10.1016/j.carbpol.2021.118138
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Identification of Unique Peptides for SARS-CoV-2 Diagnostics and Vaccine Development by an

Kesarwani, Veerbhan / Gupta, Rupal / Vetukuri, Ramesh Raju / Kushwaha, Sandeep Kumar / Gandhi, Sonu

Frontiers in immunology

2021 Volume 12, Page(s) 725240

Abstract: Ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus strains is posing new COVID-19 diagnosis and treatment challenges. To help efforts to meet these challenges we examined data acquired from proteomic analyses of human ...

Abstract	Ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus strains is posing new COVID-19 diagnosis and treatment challenges. To help efforts to meet these challenges we examined data acquired from proteomic analyses of human SARS-CoV-2-infected cell lines and samples from COVID-19 patients. Initially, 129 unique peptides were identified, which were rigorously evaluated for repeats, disorders, polymorphisms, antigenicity, immunogenicity, toxicity, allergens, sequence similarity to human proteins, and contributions from other potential cross-reacting pathogenic species or the human saliva microbiome. We also screened SARS-CoV-2-infected NBHE and A549 cell lines for presence of antigenic peptides, and identified paratope peptides from crystal structures of SARS-CoV-2 antigen-antibody complexes. We then selected four antigen peptides for docking with known viral unbound T-cell receptor (TCR), class I and II peptide major histocompatibility complex (pMHC), and identified paratope sequences. We also tested the paratope binding affinity of SARS-CoV T- and B-cell peptides that had been previously experimentally validated. The resultant antigenic peptides have high potential for generating SARS-CoV-2-specific antibodies, and the paratope peptides can be directly used to develop a COVID-19 diagnostics assay. The presented genomics and proteomics-based
MeSH term(s)	A549 Cells ; COVID-19/diagnosis ; COVID-19/immunology ; COVID-19 Vaccines/immunology ; Cell Line ; Coronavirus Nucleocapsid Proteins/genetics ; Coronavirus Nucleocapsid Proteins/metabolism ; Epitope Mapping ; Epitopes, B-Lymphocyte/genetics ; Epitopes, B-Lymphocyte/metabolism ; Epitopes, T-Lymphocyte/genetics ; Epitopes, T-Lymphocyte/metabolism ; HLA Antigens/metabolism ; Humans ; Molecular Docking Simulation ; Peptides/genetics ; Peptides/metabolism ; Phosphoproteins/genetics ; Phosphoproteins/metabolism ; Protein Binding ; Proteomics ; Pulmonary Alveoli/pathology ; Receptors, Antigen/metabolism ; SARS-CoV-2/physiology ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	COVID-19 Vaccines ; Coronavirus Nucleocapsid Proteins ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; HLA Antigens ; Peptides ; Phosphoproteins ; Receptors, Antigen ; Spike Glycoprotein, Coronavirus ; nucleocapsid phosphoprotein, SARS-CoV-2 ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-09-24
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2021.725240
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