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Article ; Online: Peripheral blood mononuclear cells - Can they provide a clue to the pathogenesis of Graves' Orbitopathy?

Basak, Madhurima / Sanyal, Tamalika / Kar, Anish / Bhattacharjee, Pritha / Das, Madhusudan / Chowdhury, Subhankar

2021 Volume 75, Issue 2, Page(s) 447–455

Abstract: Purpose: Graves' disease (GD) is an autoimmune disorder affecting primarily the thyroid gland. The most common extrathyroidal manifestation of GD is known as Graves' orbitopathy (GO). Bone marrow-derived fibrocytes represent a subset of monocytes in ... ...

Abstract	Purpose: Graves' disease (GD) is an autoimmune disorder affecting primarily the thyroid gland. The most common extrathyroidal manifestation of GD is known as Graves' orbitopathy (GO). Bone marrow-derived fibrocytes represent a subset of monocytes in peripheral blood mononuclear cells (PBMCs), infiltrate the orbital tissues, and contribute to the pathogenesis of GO. Hence objectives of the study included whether the concentration of fibrocytes in peripheral blood was higher in GO, whether TSHR m RNA expression and TSHR surface expression in peripheral blood were higher in GO in comparison to Graves' Disease (GD) and Control subjects. Methods: The percentage of circulating fibrocytes (FC) along with TSHR on its cell surface (CD 34 Result: The concentration of circulating fibrocytes was significantly higher in GO compared to GD and control [GO 17% vs GD 3% vs control 0.7% (p < 0.05)]. Moreover, these fibrocytes express a significantly higher level of TSHR in GO. This was corroborated by the measure of TSH mRNA; in GD it was 2.3-fold higher and in GO it was 3.9 fold higher than in control, in GO this transcript level was 1.7fold higher than GD (p < 0.05). TSHR Conclusion: This study sheds further light on the pathogenesis of GO.
MeSH term(s)	Graves Disease/metabolism ; Graves Ophthalmopathy/metabolism ; Humans ; Leukocytes, Mononuclear/metabolism ; Leukocytes, Mononuclear/pathology ; Receptors, Thyrotropin
Chemical Substances	Receptors, Thyrotropin
Language	English
Publishing date	2021-09-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	1194484-5
ISSN	1559-0100 ; 1355-008X ; 0969-711X
ISSN (online)	1559-0100
ISSN	1355-008X ; 0969-711X
DOI	10.1007/s12020-021-02865-0
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Article ; Online: In silico designing of vaccine candidate against Clostridium difficile.

Basak, Srijita / Deb, Debashrito / Narsaria, Utkarsh / Kar, Tamalika / Castiglione, Filippo / Sanyal, Indraneel / Bade, Pratap D / Srivastava, Anurag P

Scientific reports

2021 Volume 11, Issue 1, Page(s) 14215

Abstract: Clostridium difficile is a spore-forming gram-positive bacterium, recognized as the primary cause of antibiotic-associated nosocomial diarrhoea. Clostridium difficile infection (CDI) has emerged as a major health-associated infection with increased ... ...

Abstract	Clostridium difficile is a spore-forming gram-positive bacterium, recognized as the primary cause of antibiotic-associated nosocomial diarrhoea. Clostridium difficile infection (CDI) has emerged as a major health-associated infection with increased incidence and hospitalization over the years with high mortality rates. Contamination and infection occur after ingestion of vegetative spores, which germinate in the gastro-intestinal tract. The surface layer protein and flagellar proteins are responsible for the bacterial colonization while the spore coat protein, is associated with spore colonization. Both these factors are the main concern of the recurrence of CDI in hospitalized patients. In this study, the CotE, SlpA and FliC proteins are chosen to form a multivalent, multi-epitopic, chimeric vaccine candidate using the immunoinformatics approach. The overall reliability of the candidate vaccine was validated in silico and the molecular dynamics simulation verified the stability of the vaccine designed. Docking studies showed stable vaccine interactions with Toll-Like Receptors of innate immune cells and MHC receptors. In silico codon optimization of the vaccine and its insertion in the cloning vector indicates a competent expression of the modelled vaccine in E. coli expression system. An in silico immune simulation system evaluated the effectiveness of the candidate vaccine to trigger a protective immune response.
MeSH term(s)	Bacterial Vaccines/immunology ; Bacterial Vaccines/therapeutic use ; Clostridioides difficile/immunology ; Clostridioides difficile/pathogenicity ; Clostridium Infections/drug therapy ; Clostridium Infections/immunology ; Computational Biology/methods ; Escherichia coli/metabolism ; Humans
Chemical Substances	Bacterial Vaccines
Language	English
Publishing date	2021-07-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-93305-6
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Article ; Online: Immunoinformatics based designing a multi-epitope vaccine against pathogenic Chandipura vesiculovirus.

Deb, Debashrito / Basak, Srijita / Kar, Tamalika / Narsaria, Utkarsh / Castiglione, Filippo / Paul, Abhirup / Pandey, Ashutosh / Srivastava, Anurag P

Journal of cellular biochemistry

2021 Volume 123, Issue 2, Page(s) 322–346

Abstract: Chandipura vesiculovirus (CHPV) is a rapidly emerging pathogen responsible for causing acute encephalitis. Due to its widespread occurrence in Asian and African countries, this has become a global threat, and there is an urgent need to design an ... ...

Abstract	Chandipura vesiculovirus (CHPV) is a rapidly emerging pathogen responsible for causing acute encephalitis. Due to its widespread occurrence in Asian and African countries, this has become a global threat, and there is an urgent need to design an effective and nonallergenic vaccine against this pathogen. The present study aimed to develop a multi-epitope vaccine using an immunoinformatics approach. The conventional method of vaccine design involves large proteins or whole organism which leads to unnecessary antigenic load with increased chances of allergenic reactions. In addition, the process is also very time-consuming and labor-intensive. These limitations can be overcome by peptide-based vaccines comprising short immunogenic peptide fragments that can elicit highly targeted immune responses, avoiding the chances of allergenic reactions, in a relatively shorter time span. The multi-epitope vaccine constructed using CTL, HTL, and IFN-γ epitopes was able to elicit specific immune responses when exposed to the pathogen, in silico. Not only that, molecular docking and molecular dynamics simulation studies confirmed a stable interaction of the vaccine with the immune receptors. Several physicochemical analyses of the designed vaccine candidate confirmed it to be highly immunogenic and nonallergic. The computer-aided analysis performed in this study suggests that the designed multi-epitope vaccine can elicit specific immune responses and can be a potential candidate against CHPV.
MeSH term(s)	Epitopes, B-Lymphocyte/chemistry ; Epitopes, B-Lymphocyte/immunology ; Epitopes, T-Lymphocyte/chemistry ; Epitopes, T-Lymphocyte/immunology ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Rhabdoviridae Infections/immunology ; Vaccines, Subunit/chemistry ; Vaccines, Subunit/immunology ; Vesiculovirus/chemistry ; Vesiculovirus/immunology ; Viral Vaccines/chemistry ; Viral Vaccines/immunology
Chemical Substances	Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Vaccines, Subunit ; Viral Vaccines
Language	English
Publishing date	2021-11-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	392402-6
ISSN	1097-4644 ; 0730-2312
ISSN (online)	1097-4644
ISSN	0730-2312
DOI	10.1002/jcb.30170
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: In silico designing of vaccine candidate against Clostridium difficile

Srijita Basak / Debashrito Deb / Utkarsh Narsaria / Tamalika Kar / Filippo Castiglione / Indraneel Sanyal / Pratap D. Bade / Anurag P. Srivastava

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 22

Abstract: Abstract Clostridium difficile is a spore-forming gram-positive bacterium, recognized as the primary cause of antibiotic-associated nosocomial diarrhoea. Clostridium difficile infection (CDI) has emerged as a major health-associated infection with ... ...

Abstract	Abstract Clostridium difficile is a spore-forming gram-positive bacterium, recognized as the primary cause of antibiotic-associated nosocomial diarrhoea. Clostridium difficile infection (CDI) has emerged as a major health-associated infection with increased incidence and hospitalization over the years with high mortality rates. Contamination and infection occur after ingestion of vegetative spores, which germinate in the gastro-intestinal tract. The surface layer protein and flagellar proteins are responsible for the bacterial colonization while the spore coat protein, is associated with spore colonization. Both these factors are the main concern of the recurrence of CDI in hospitalized patients. In this study, the CotE, SlpA and FliC proteins are chosen to form a multivalent, multi-epitopic, chimeric vaccine candidate using the immunoinformatics approach. The overall reliability of the candidate vaccine was validated in silico and the molecular dynamics simulation verified the stability of the vaccine designed. Docking studies showed stable vaccine interactions with Toll‐Like Receptors of innate immune cells and MHC receptors. In silico codon optimization of the vaccine and its insertion in the cloning vector indicates a competent expression of the modelled vaccine in E. coli expression system. An in silico immune simulation system evaluated the effectiveness of the candidate vaccine to trigger a protective immune response.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A candidate multi-epitope vaccine against SARS-CoV-2

Kar, Tamalika / Narsaria, Utkarsh / Basak, Srijita / Deb, Debashrito / Castiglione, Filippo / Mueller, David M. / Srivastava, Anurag P.

Scientific Reports

2020 Volume 10, Issue 1

Keywords	Multidisciplinary ; covid19
Language	English
Publisher	Springer Science and Business Media LLC
Publishing country	us
Document type	Article ; Online
ZDB-ID	2615211-3
ISSN	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-67749-1
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Article ; Online: A candidate multi-epitope vaccine against SARS-CoV-2

Tamalika Kar / Utkarsh Narsaria / Srijita Basak / Debashrito Deb / Filippo Castiglione / David M. Mueller / Anurag P. Srivastava

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 130

Abstract: Abstract In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another ... ...

Abstract	Abstract In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another coronavirus, SARS-CoV-2, with a high fatality rate. The spike glycoprotein of SARS-CoV-2 mediates entry of virus into the host cell and is one of the most important antigenic determinants, making it a potential candidate for a vaccine. In this study, we have computationally designed a multi-epitope vaccine using spike glycoprotein of SARS-CoV-2. The overall quality of the candidate vaccine was validated in silico and Molecular Dynamics Simulation confirmed the stability of the designed vaccine. Docking studies revealed stable interactions of the vaccine with Toll-Like Receptors and MHC Receptors. The in silico cloning and codon optimization supported the proficient expression of the designed vaccine in E. coli expression system. The efficiency of the candidate vaccine to trigger an effective immune response was assessed by an in silico immune simulation. The computational analyses suggest that the designed multi-epitope vaccine is structurally stable which can induce specific immune responses and thus, can be a potential vaccine candidate against SARS-CoV-2.
Keywords	Medicine ; R ; Science ; Q ; covid19
Subject code	570
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A candidate multi-epitope vaccine against SARS-CoV-2.

Kar, Tamalika / Narsaria, Utkarsh / Basak, Srijita / Deb, Debashrito / Castiglione, Filippo / Mueller, David M / Srivastava, Anurag P

Scientific reports

2020 Volume 10, Issue 1, Page(s) 10895

Abstract: In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another coronavirus, SARS- ... ...

Abstract	In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another coronavirus, SARS-CoV-2, with a high fatality rate. The spike glycoprotein of SARS-CoV-2 mediates entry of virus into the host cell and is one of the most important antigenic determinants, making it a potential candidate for a vaccine. In this study, we have computationally designed a multi-epitope vaccine using spike glycoprotein of SARS-CoV-2. The overall quality of the candidate vaccine was validated in silico and Molecular Dynamics Simulation confirmed the stability of the designed vaccine. Docking studies revealed stable interactions of the vaccine with Toll-Like Receptors and MHC Receptors. The in silico cloning and codon optimization supported the proficient expression of the designed vaccine in E. coli expression system. The efficiency of the candidate vaccine to trigger an effective immune response was assessed by an in silico immune simulation. The computational analyses suggest that the designed multi-epitope vaccine is structurally stable which can induce specific immune responses and thus, can be a potential vaccine candidate against SARS-CoV-2.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Antibody Affinity/immunology ; Betacoronavirus/chemistry ; Betacoronavirus/genetics ; Betacoronavirus/immunology ; COVID-19 ; Coronavirus Infections/prevention & control ; Coronavirus Infections/virology ; Epitopes, B-Lymphocyte/immunology ; Epitopes, T-Lymphocyte/immunology ; Histocompatibility Antigens/immunology ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Pandemics/prevention & control ; Peptidyl-Dipeptidase A/metabolism ; Phylogeny ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/virology ; Protein Structure, Tertiary ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/immunology ; Spike Glycoprotein, Coronavirus/metabolism ; Toll-Like Receptor 2/immunology ; Toll-Like Receptor 2/metabolism ; Toll-Like Receptor 4/immunology ; Toll-Like Receptor 4/metabolism ; Viral Vaccines/immunology ; Viral Vaccines/metabolism
Chemical Substances	Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Histocompatibility Antigens ; Spike Glycoprotein, Coronavirus ; TLR2 protein, human ; TLR4 protein, human ; Toll-Like Receptor 2 ; Toll-Like Receptor 4 ; Viral Vaccines ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-07-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-67749-1
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Article ; Online: MAPK cascade gene family in Camellia sinensis: In-silico identification, expression profiles and regulatory network analysis.

Chatterjee, Archita / Paul, Abhirup / Unnati, G Meher / Rajput, Ruchika / Biswas, Trisha / Kar, Tamalika / Basak, Srijita / Mishra, Neelam / Pandey, Ashutosh / Srivastava, Anurag Prakash

BMC genomics

2020 Volume 21, Issue 1, Page(s) 613

Abstract: Background: Mitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in tea.: Result: In this study, ...

Abstract	Background: Mitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in tea. Result: In this study, 5 genes of Mitogen Activated Protein Kinase Kinase (MKK) and 16 genes of Mitogen Activated Protein Kinase (MPK) in Camellia sinensis were found through a genome-wide search taking Arabidopsis thaliana as the reference genome. Also, phylogenetic relationships along with structural analysis which includes gene structure, location as well as protein conserved motifs and domains, were systematically examined and further, predictions were validated by the results. The plant species taken for comparative study clearly displayed segmental duplication, which was a significant candidate for MAPK cascade expansion. Also, functional interaction was carried out in C. sinensis based on the orthologous genes in Arabidopsis. The expression profiles linked to various stress treatments revealed wide involvement of MAPK and MAPKK genes from Tea in response to various abiotic factors. In addition, the expression of these genes was analysed in various tissues. Conclusion: This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the MAPK cascade regulatory network in C. sinensis.
MeSH term(s)	Camellia sinensis/enzymology ; Camellia sinensis/genetics ; Camellia sinensis/metabolism ; Gene Expression Regulation, Plant ; Gene Regulatory Networks ; MAP Kinase Signaling System ; Mitogen-Activated Protein Kinases/genetics ; Mitogen-Activated Protein Kinases/metabolism ; Plant Proteins/genetics ; Plant Proteins/metabolism
Chemical Substances	Plant Proteins ; Mitogen-Activated Protein Kinases (EC 2.7.11.24)
Keywords	covid19
Language	English
Publishing date	2020-09-07
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-020-07030-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A candidate multi-epitope vaccine against SARS-CoV-2

Kar, Tamalika / Narsaria, Utkarsh / Basak, Srijita / Deb, Debashrito / Castiglione, Filippo / Mueller, David M / Srivastava, Anurag P

Sci Rep

Abstract	In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another coronavirus, SARS-CoV-2, with a high fatality rate. The spike glycoprotein of SARS-CoV-2 mediates entry of virus into the host cell and is one of the most important antigenic determinants, making it a potential candidate for a vaccine. In this study, we have computationally designed a multi-epitope vaccine using spike glycoprotein of SARS-CoV-2. The overall quality of the candidate vaccine was validated in silico and Molecular Dynamics Simulation confirmed the stability of the designed vaccine. Docking studies revealed stable interactions of the vaccine with Toll-Like Receptors and MHC Receptors. The in silico cloning and codon optimization supported the proficient expression of the designed vaccine in E. coli expression system. The efficiency of the candidate vaccine to trigger an effective immune response was assessed by an in silico immune simulation. The computational analyses suggest that the designed multi-epitope vaccine is structurally stable which can induce specific immune responses and thus, can be a potential vaccine candidate against SARS-CoV-2.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #629396
Database	COVID19

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Article: MAPK cascade gene family in Camellia sinensis: In-silico identification, expression profiles and regulatory network analysis

Chatterjee, Archita / Paul, Abhirup / Unnati, G Meher / Rajput, Ruchika / Biswas, Trisha / Kar, Tamalika / Basak, Srijita / Mishra, Neelam / Pandey, Ashutosh / Srivastava, Anurag Prakash

BMC Genomics

Abstract: BACKGROUND: Mitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in tea. RESULT: In this study, 5 ... ...

Abstract	BACKGROUND: Mitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in tea. RESULT: In this study, 5 genes of Mitogen Activated Protein Kinase Kinase (MKK) and 16 genes of Mitogen Activated Protein Kinase (MPK) in Camellia sinensis were found through a genome-wide search taking Arabidopsis thaliana as the reference genome. Also, phylogenetic relationships along with structural analysis which includes gene structure, location as well as protein conserved motifs and domains, were systematically examined and further, predictions were validated by the results. The plant species taken for comparative study clearly displayed segmental duplication, which was a significant candidate for MAPK cascade expansion. Also, functional interaction was carried out in C. sinensis based on the orthologous genes in Arabidopsis. The expression profiles linked to various stress treatments revealed wide involvement of MAPK and MAPKK genes from Tea in response to various abiotic factors. In addition, the expression of these genes was analysed in various tissues. CONCLUSION: This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the MAPK cascade regulatory network in C. sinensis.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #32894062
Database	COVID19

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