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Bioinformatics Tools for the Detection and Identification of Mechanisms in...
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Bioinformatics Tools for the Detection and Identification of Mechanisms in Immune Cells of COVID-19

A special issue of Immuno (ISSN 2673-5601).

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 34303

Special Issue Editors

Dr. Saurabh Kumar Jha

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Guest Editor
Department of Biotechnology, Sharda University, Greater Noida, India
Interests: natural products; cell signaling; human health and disease; stem cell and regenerative medicine; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Niraj Kumar Jha

E-Mail Website
Guest Editor
Department of Biotechnology, Sharda University, Greater Noida, India
Interests: natural products; neurodegenerative disorders; neuro oncology; signalling and neurotherapeutics
Special Issues, Collections and Topics in MDPI journals
Dr. Parma Nand

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Guest Editor
School of Engineering and Technology, Sharda University, Greater Noida 201310, India
Interests: computational biology; integrative bioscience; cyber security & business/data analytics
Dr. Kavindra K. Kesari

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Guest Editor
Department of Applied Physics, Aalto University, Espoo 00076, Finland
Interests: testicular cancer; infertility; Alzheimer’s disease; cancer therapeutic; neurotoxicity; brain cancer; nanoparticle research; radiation research; bioinformatics; cell and structural biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bioinformatics is playing a pivotal role in biomedical sciences and, therefore, revolutionizing healthcare by providing platforms for comparison and identification of genetic signatures. We are seeing a surge of tools that offer different insights into mechanisms to better understand the underlying biological phenomenon.

Bioinformatics tools provide a list of options that can answer immunological questions and challenges such as obtaining structural information, gene expression patterns, genetic variation across populations, functions of particular subsets of immune cells, and, most importantly, to generate an informed hypothesis or prediction that can be tested bench-side. In this research topic, we would like to recognize such outstanding bioinformatics analyses and tools that are particularly designed to provide a deeper insight into the role of immune cells in Covid-19.

This Special Issue should encompass all disorders that involve Covid-19 and along with the direct involvement of the immune system in this disease. We are also interested in understanding whether drugs with immunological targets can affect Covid-19 and related disorders. The research topic will focus on, but is not be limited to, the following:

  1. Tools designed to visualize the genetic and immune profiles of Covid-19;
  2. Computational analysis of immunogenic patterns in Covid-19;
  3. Investigation of a novel question relating to Covid-19 and immunology using bioinformatics tools;
  4. Reviews to summarize the current knowledge in the field of bioinformatics tools in Covid-19;
  5. Databases developed for Covid-19.

The broad readership of this journal will attract a lot of scientists from all over the world to contribute to this collection.

Dr. Saurabh Kumar Jha
Dr. Niraj Kumar Jha
Dr. Parma Nand
Dr. Kavindra Kumar Kesari
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Immuno is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Covid-19
  • bioinformatics tools
  • Immune profiles
  • immunology
  • Computational genomics
  • gene signature

Published Papers (4 papers)

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Review

28 pages, 1441 KiB  
Review
Probing the Immune System Dynamics of the COVID-19 Disease for Vaccine Designing and Drug Repurposing Using Bioinformatics Tools
by Deepshikha Yadav, Shriya Agarwal, Pranav Pancham, Divya Jindal, Vinayak Agarwal, Premshankar Kumar Dubey, Saurabh K. Jha, Shalini Mani, Rachana, Abhijit Dey, Niraj Kumar Jha, Kavindra Kumar Kesari and Manisha Singh
Immuno 2022, 2(2), 344-371; https://0-doi-org.brum.beds.ac.uk/10.3390/immuno2020022 - 28 Apr 2022
Cited by 2 | Viewed by 5412
Abstract
The pathogenesis of COVID-19 is complicated by immune dysfunction. The impact of immune-based therapy in COVID-19 patients has been well documented, with some notable studies on the use of anti-cytokine medicines. However, the complexity of disease phenotypes, patient heterogeneity and the varying quality [...] Read more.
The pathogenesis of COVID-19 is complicated by immune dysfunction. The impact of immune-based therapy in COVID-19 patients has been well documented, with some notable studies on the use of anti-cytokine medicines. However, the complexity of disease phenotypes, patient heterogeneity and the varying quality of evidence from immunotherapy studies provide problems in clinical decision-making. This review seeks to aid therapeutic decision-making by giving an overview of the immunological responses against COVID-19 disease that may contribute to the severity of the disease. We have extensively discussed theranostic methods for COVID-19 detection. With advancements in technology, bioinformatics has taken studies to a higher level. The paper also discusses the application of bioinformatics and machine learning tools for the diagnosis, vaccine design and drug repurposing against SARS-CoV-2. Full article
(This article belongs to the Special Issue Bioinformatics Tools for the Detection and Identification of Mechanisms in Immune Cells of COVID-19)
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15 pages, 1267 KiB  
Review
Immunological Mechanisms of Vaccine-Induced Protection against SARS-CoV-2 in Humans
by Keshav Goyal, Harsh Goel, Pritika Baranwal, Anisha Tewary, Aman Dixit, Avanish Kumar Pandey, Mercilena Benjamin, Pranay Tanwar, Abhijit Dey, Fahad Khan, Pratibha Pandey, Piyush Kumar Gupta, Dhruv Kumar, Shubhadeep Roychoudhury, Niraj Kumar Jha, Tarun Kumar Upadhyay and Kavindra Kumar Kesari
Immuno 2021, 1(4), 442-456; https://0-doi-org.brum.beds.ac.uk/10.3390/immuno1040032 - 15 Nov 2021
Cited by 7 | Viewed by 8295
Abstract
The SARS-CoV-2 infection spread rapidly throughout the world and appears to involve in both humoral and cell-mediated immunity. SARS-CoV-2 is attached to host cells via binding to the viral spike (S) proteins and its cellular receptors angiotensin-converting enzyme 2 (ACE2). Consequently, the S [...] Read more.
The SARS-CoV-2 infection spread rapidly throughout the world and appears to involve in both humoral and cell-mediated immunity. SARS-CoV-2 is attached to host cells via binding to the viral spike (S) proteins and its cellular receptors angiotensin-converting enzyme 2 (ACE2). Consequently, the S protein is primed with serine proteases TMPRSS2 and TMPRSS4, which facilitate the fusion of viral and cellular membranes result in the entry of viral RNA into the host cell. Vaccines are urgently required to combat the coronavirus disease 2019 (COVID-19) outbreak and aid in the recovery to pre-pandemic levels of normality. The long-term protective immunity is provided by the vaccine antigen (or pathogen)-specific immune effectors and the activation of immune memory cells that can be efficiently and rapidly reactivated upon pathogen exposure. Research efforts aimed towards the design and development of vaccines for SARS-CoV-2 are increasing. Numerous coronavirus disease 2019 (COVID-19) vaccines have passed late-stage clinical investigations with promising outcomes. This review focuses on the present state and future prospects of COVID-19 vaccines research and development, with a particular emphasis on immunological mechanisms of various COVID-19vaccines such as adenoviral vector-based vaccines, mRNA vaccines, and DNA vaccines that elicits immunological responses against SARS-CoV-2 infections in humans. Full article
(This article belongs to the Special Issue Bioinformatics Tools for the Detection and Identification of Mechanisms in Immune Cells of COVID-19)
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20 pages, 1636 KiB  
Review
Cannabinoid Type-2 Receptor Agonist, JWH133 May Be a Possible Candidate for Targeting Infection, Inflammation, and Immunity in COVID-19
by Niraj Kumar Jha, Charu Sharma, Mohamed Fizur Nagoor Meeran, Saurabh Kumar Jha, Vivek Dhar Dwivedi, Piyush Kumar Gupta, Abhijit Dey, Kavindra Kumar Kesari and Shreesh Ojha
Immuno 2021, 1(3), 285-304; https://0-doi-org.brum.beds.ac.uk/10.3390/immuno1030020 - 30 Aug 2021
Viewed by 3058
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, is a deadly disease affecting millions due to the non-availability of drugs and vaccines. The majority of COVID-19 drugs have been repurposed based on antiviral, immunomodulatory, and antibiotic potential. The pathogenesis and advanced complications with infection involve [...] Read more.
The COVID-19 pandemic, caused by SARS-CoV-2, is a deadly disease affecting millions due to the non-availability of drugs and vaccines. The majority of COVID-19 drugs have been repurposed based on antiviral, immunomodulatory, and antibiotic potential. The pathogenesis and advanced complications with infection involve the immune-inflammatory cascade. Therefore, a therapeutic strategy could reduce infectivity, inflammation, and immune modulation. In recent years, modulating the endocannabinoid system, particularly activation of the cannabinoid type 2 (CB2) receptor is a promising therapeutic target for modulation of immune-inflammatory responses. JWH133, a selective, full functional agonist of the CB2 receptor, has been extensively studied for its potent anti-inflammatory, antiviral, and immunomodulatory properties. JWH133 modulates numerous signaling pathways and inhibits inflammatory mediators, including cytokines, chemokines, adhesion molecules, prostanoids, and eicosanoids. In this study, we propose that JWH133 could be a promising candidate for targeting infection, immunity, and inflammation in COVID-19, due to its pharmacological and molecular mechanisms in numerous preclinical efficacy and safety studies, along with its immunomodulatory, anti-inflammatory, organoprotective, and antiviral properties. Thus, JWH133 should be investigated in preclinical and clinical studies for its potential as an agent or adjuvant with other agents for its effect on viremia, infectivity, immune modulation, resolution of inflammation, reduction in severity, and progression of complications in COVID-19. JWH133 is devoid of psychotropic effects due to CB2 receptor selectivity, has negligible toxicity, good bioavailability and druggable properties, including pharmacokinetic and physicochemical effects. We believe that JWH133 could be a promising drug and may inspire further studies for an evidence-based approach against COVID-19. Full article
(This article belongs to the Special Issue Bioinformatics Tools for the Detection and Identification of Mechanisms in Immune Cells of COVID-19)
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37 pages, 3252 KiB  
Review
Current Understanding of Novel Coronavirus: Molecular Pathogenesis, Diagnosis, and Treatment Approaches
by Niraj Kumar Jha, Madhan Jeyaraman, Mahesh Rachamalla, Shreesh Ojha, Kamal Dua, Dinesh Kumar Chellappan, Sathish Muthu, Ankur Sharma, Saurabh Kumar Jha, Rashmi Jain, Naveen Jeyaraman, Prajwal GS, Rohit Satyam, Fahad Khan, Pratibha Pandey, Nitin Verma, Sandeep Kumar Singh, Shubhadeep Roychoudhury, Sunny Dholpuria, Janne Ruokolainen and Kavindra Kumar Kesariadd Show full author list remove Hide full author list
Immuno 2021, 1(1), 30-66; https://0-doi-org.brum.beds.ac.uk/10.3390/immuno1010004 - 26 Mar 2021
Cited by 17 | Viewed by 15783
Abstract
An outbreak of “Pneumonia of Unknown Etiology” occurred in Wuhan, China, in late December 2019. Later, the agent factor was identified and coined as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the disease was named coronavirus disease 2019 (COVID-19). In a shorter [...] Read more.
An outbreak of “Pneumonia of Unknown Etiology” occurred in Wuhan, China, in late December 2019. Later, the agent factor was identified and coined as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the disease was named coronavirus disease 2019 (COVID-19). In a shorter period, this newly emergent infection brought the world to a standstill. On 11 March 2020, the WHO declared COVID-19 as a pandemic. Researchers across the globe have joined their hands to investigate SARS-CoV-2 in terms of pathogenicity, transmissibility, and deduce therapeutics to subjugate this infection. The researchers and scholars practicing different arts of medicine are on an extensive quest to come up with safer ways to curb the pathological implications of this viral infection. A huge number of clinical trials are underway from the branch of allopathy and naturopathy. Besides, a paradigm shift on cellular therapy and nano-medicine protocols has to be optimized for better clinical and functional outcomes of COVID-19-affected individuals. This article unveils a comprehensive review of the pathogenesis mode of spread, and various treatment modalities to combat COVID-19 disease. Full article
(This article belongs to the Special Issue Bioinformatics Tools for the Detection and Identification of Mechanisms in Immune Cells of COVID-19)
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