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Pathogens
Special Issues
SARS-CoV-2 Research from an Interdisciplinary and Holistic View
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SARS-CoV-2 Research from an Interdisciplinary and Holistic View

A special issue of Pathogens (ISSN 2076-0817).

Deadline for manuscript submissions: closed (30 December 2023) | Viewed by 4015

Special Issue Editors

Prof. Dr. José Hélio Costa

E-Mail Website1 Website2
Guest Editor
1. Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60451-970, Ceara, Brazil
2. Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
Interests: genetics; plant molecular biology; the identification of potential genes for biotechnological applications; the molecular basis associated with biochemistry and the physiological responses of plants under stress
Special Issues, Collections and Topics in MDPI journals
Dr. Carlos Noceda

E-Mail Website
Guest Editor
1. Biotecnología Celular y Molecular de Plantas (BIOCEMP)/Biotecnología Industrial, Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Av. General Rumiñahui s/n., P.O. Box 171-5-231B, Sangolquí 171103, Ecuador
2. Facultad de Ingeniería, Universidad Estatal de Milagro (UNEMI), Milagro 091050, Guayas, Ecuador
3. Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, 3400-641 Alentejo, Portugal
Interests: cell reprogramming; epigenetics; evolution; stress
Dr. Birgit Arnholdt-Schmitt

E-Mail
Guest Editor
1. Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Alentejo, Portugal
2. Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
Interests: functional marker research on plasticity in plants and humans that links to adaptive robustness; prediction of resilient performance from early cell reprogramming; research on SARS-CoV-2 variants

Special Issue Information

Dear Colleagues,

Reactive oxygen species (ROS) signaling is widely accepted as a relevant sensor for environment–organism communication. Abiotic and biotic environmental changes, including viral threats, induce ROS signaling that starts at the cell membrane of primary target cells and subsequently infiltrates into the cellular redox network, where mitochondrial respiration plays a central role in regulation. Immunometabolism research typically focuses on the interplay between energy metabolism and biochemical pathways in order to identify their influence on the functionality of innate and adaptive components of the classical immune system. However, whether resilience signaling begins earlier than suspected or microbiota play a possible role in this process remains unknown. This Special Issue aims to collect research aiding the understanding of early metabolic responses and their drivers in primary target cells upon viral attacks linked to resilience. Special attention will be given to research related to SARS-CoV-2 variants. We welcome high-quality human, animal and plant research strictly relevant to this topic from across all types of disciplines, including clinical observations advancing current knowledge with new approaches. Manuscripts may be brief reports, communications, research articles, opinion papers and reviews that provide novel perspectives [1–11]. 

Relevant Recent Publications:

  1. Arnholdt-Schmitt, B.; Mohanapriya, G.; Bharadwaj, R.; Noceda, C.; Macedo, E.S.; Sathishkumar, R.; Gupta, K.J.; Sircar, D.; Kumar, S.R.; Srivastava, S.; et al. From Plant Survival Under Severe Stress to Anti-Viral Human Defense − A Perspective That Calls for Common Efforts. Front. Immunol. 2021, 12, 673723. doi: 10.3389/fimmu.2021.673723.
  2. Costa, J.H.; Mohanapriya, G.; Bharadwaj, R.; Noceda, C.; Thiers, K.L.L.; Aziz, S.; Srivastava, S.; Oliveira, M.; Gupta, K.J.; Kumari, A. Sircar, D.; Kumar, S.R.; Achra, A.; Sathishkumar, R.; Adholeya, A.; Arnholdt-Schmitt, B. ROS/RNS Balancing, Aerobic Fermentation Regulation and Cell Cycle Control - a Complex Early Trait ('CoV-MAC-TED') for Combating SARS-CoV-2-Induced Cell Reprogramming. Front Immunol. 2021, 12, 673692. doi: 10.3389/fimmu.2021.673692.
  3. Bharadwaj, R.; Noceda, C.; Mohanapriya, G.; Kumar, S.R.;Thiers, K.L.L.; Costa, J.H.; Macedo, E.S.; Kumari, A.; Gupta, K.J.; Srivastava, S.; Adholeya, A.; Oliveira, M.; Velada, I.; Sircar, D.; Sathishkumar, R.; Arnholdt-Schmitt, B. Adaptive Reprogramming During Early Seed Germination Requires Temporarily Enhanced Fermentation-A Critical Role for Alternative Oxidase Regulation That Concerns Also Microbiota Effectiveness. Front. Plant Sci. 2021, 12, 686274. doi: 10.3389/fpls.2021.686274
  4. Mohanapriya, G.; Bharadwaj, R.; Noceda, C.; Costa, J.H.; Kumar, S.R.; Sathishkumar, R.; Thiers, K.L.L.; Santos Macedo, E.; Silva, S.; Annicchiarico, P.; Groot, S.P.C.; Kodde, J.; Kumari, A.; Gupta, K.J.; Arnholdt-Schmitt, B. Alternative Oxidase (AOX) Senses Stress Levels to Coordinate Auxin-Induced Reprogramming From Seed Germination to Somatic Embryogenesis — A Role Relevant for Seed Vigor Prediction and Plant Robustness. Front. Plant Sci. 2019, 10, 1134. doi: 10.3389/fpls.2019.01134
  5. Costa, J.H.; Aziz, S.; Noceda, C.; Arnholdt-Schmitt, B. Major Complex Trait for Early De Novo Programming 'CoV-MAC-TED' Detected in Human Nasal Epithelial Cells Infected by Two SARS-CoV-2 Variants Is Promising to Help in Designing Therapeutic Strategies. Vaccines (Basel) 2021, 9, 1399. doi: 10.3390/vaccines9121399.
  6. Costa, J.H.; Aziz, S.; Noceda, C.; Arnholdt-Schmitt, B. (2021b, preprint) Transcriptome data from human nasal epithelial cells infected by H3N2 influenza virus indicate early unbalanced ROS/RNA levels, temporarily increased aerobic fermentation linked to enhanced α-tubulin and rapid energy-dependent IRF9-marked immunization. bioRxiv 2021b, preprint. https://doi.org/10.1101/2021.10.18.464828
  7. Arnholdt-Schmitt, B.; Aziz, S.; Costa, J.H. Allelic Gene Polymorphisms Suspected to Diversify the Individual Early Metabolic Response Upon Influenza H3N2 and SARS-CoV-2 Infections. IDDB 2022. doi:10.36401/IDDB-22-01.
  8. Ferreira, A.O.; Cardoso, H.G.; Macedo, E.S.; Breviario, D.; Arnholdt-Schmitt, B. Intron Polymorphism Pattern in AOX1b of Wild St John’s Wort (Hypericum Perforatum) Allows Discrimination Between Individual Plants. Physiol Plant (2009) 137(4):520–531. DOI: 10.1111/j.1399-3054.2009.01291.x
  9. Arnholdt-Schmitt, B.; Valadas, V.; and Döring, M. (2014). Functional marker development is challenged by the ubiquity of endophytes—a practical perspective. Brief. Funct. Genomics 15(1), 16–21. DOI: 10.1093/bfgp/elu049
  10. Arnholdt-Schmitt, B.; Aziz, S.; Costa, J.H. Efficient Rebalancing of ROS Levels in Plants Links to Temporarily Enhanced Aerobic Fermentation, Distinct Cell Restructuration, and Resilience in Field. IDDB 2022. doi:10.36401/IDDB-22-02.
  11. Arnholdt-Schmitt, B.; Aziz, S.; Costa, J.H. Diversity Control in Early Transcribed ROS/RNS-balancing Genes: A Common Mechanism for Healthy Resilience? IDDB 2022. doi:10.36401/IDDB-22-03.

Prof. Dr. José Hélio Costa
Dr. Carlos Noceda
Dr. Birgit Arnholdt-Schmitt
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. Pathogens is an international peer-reviewed open access monthly 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 2700 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

  • individual virus tolerance
  • SARS-CoV-2 variants
  • early ROS signaling and adaptive robustness
  • ROS/RNS balancing
  • genetic markers
  • biomarkers
  • marker-assisted resilience prediction
  • microbiota
  • translational research
  • in vitro cell tests
  • individualized medicine
  • nomenclature of immunological terms
  • plasticity and health
  • interdisciplinary/holistic research
  • interdisciplinary/holistic education

Published Papers (2 papers)

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Research

20 pages, 2651 KiB  
Article
Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways
by Eric Petterson Viana Pereira, Stela Mirla da Silva Felipe, Raquel Martins de Freitas, José Ednésio da Cruz Freire, Antonio Edson Rocha Oliveira, Natália Canabrava, Paula Matias Soares, Mauricio Fraga van Tilburg, Maria Izabel Florindo Guedes, Chad Eric Grueter and Vânia Marilande Ceccatto
Pathogens 2023, 12(11), 1373; https://doi.org/10.3390/pathogens12111373 - 20 Nov 2023
Cited by 1 | Viewed by 1516
Abstract
The COVID-19 disease, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), emerged in late 2019 and rapidly spread worldwide, becoming a pandemic that infected millions of people and caused significant deaths. COVID-19 continues to be a major threat, and there is [...] Read more.
The COVID-19 disease, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), emerged in late 2019 and rapidly spread worldwide, becoming a pandemic that infected millions of people and caused significant deaths. COVID-19 continues to be a major threat, and there is a need to deepen our understanding of the virus and its mechanisms of infection. To study the cellular responses to SARS-CoV-2 infection, we performed an RNA sequencing of infected vs. uninfected Calu-3 cells. Total RNA was extracted from infected (0.5 MOI) and control Calu-3 cells and converted to cDNA. Sequencing was performed, and the obtained reads were quality-analyzed and pre-processed. Differential expression was assessed with the EdgeR package, and functional enrichment was performed in EnrichR for Gene Ontology, KEGG pathways, and WikiPathways. A total of 1040 differentially expressed genes were found in infected vs. uninfected Calu-3 cells, of which 695 were up-regulated and 345 were down-regulated. Functional enrichment analyses revealed the predominant up-regulation of genes related to innate immune response, response to virus, inflammation, cell proliferation, and apoptosis. These transcriptional changes following SARS-CoV-2 infection may reflect a cellular response to the infection and help to elucidate COVID-19 pathogenesis, in addition to revealing potential biomarkers and drug targets. Full article
(This article belongs to the Special Issue SARS-CoV-2 Research from an Interdisciplinary and Holistic View)
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12 pages, 482 KiB  
Article
Correlation between Clinical and Immunological Variables and Humoral Response to SARS-CoV-2 Vaccination in Adult Patients with Antibody Deficiency Disorders
by Carmen Bracke, Cristina Miranda, Sandra González, Irma Casas, Pere Joan Cardona, Rosa Maria Benitez, Nieves Sopena, Esteban Alberto Reynaga, Marta Massanella, Bonaventura Clotet, Jorge Carrillo, Lourdes Mateu and Maria Luisa Pedro-Botet
Pathogens 2022, 11(11), 1364; https://doi.org/10.3390/pathogens11111364 - 16 Nov 2022
Cited by 1 | Viewed by 1586
Abstract
Background. Prophylactic vaccination has proven to be the most effective strategy to fight the COVID-19 pandemic. Methods. This was a prospective observational cohort study involving 30 predominantly antibody deficiency disorders (ADD)-afflicted adult patients on immunoglobulin replacement therapy vaccinated with three doses of the [...] Read more.
Background. Prophylactic vaccination has proven to be the most effective strategy to fight the COVID-19 pandemic. Methods. This was a prospective observational cohort study involving 30 predominantly antibody deficiency disorders (ADD)-afflicted adult patients on immunoglobulin replacement therapy vaccinated with three doses of the mRNA-1273 COVID-19 vaccine, and 10 healthy controls. Anti-RBD IgG antibodies were determined in plasma samples collected just before the first dose of mRNA-based COVID-19 vaccine and on weeks 4, 8, 24, and 28 following the first vaccination. Patients were categorized based on the levels of anti-RBD antibodies determined on w8 as non-, low-, and responders. Chi-square and Kruskal–Wallis tests were used to see if any variables correlated with humoral response levels. Any adverse effects of the mRNA-based vaccine were also noted. Results. The COVID-19 vaccine was safe and well-tolerated. The humoral response elicited at w8 after vaccination depended on the type of ADD, the type of immunoglobulin deficiency, the presence of granulomatous lymphocytic interstitial lung disease, recent use of immunosuppressive drugs, and the switched memory B cells counts. The third vaccine dose boosted humoral response in previous responders to second dose but seldom in non-responders. Conclusions: The humoral response of patients with predominant ADD depends mostly on the type of immunodeficiency and on the frequency of B and T cell populations. Full article
(This article belongs to the Special Issue SARS-CoV-2 Research from an Interdisciplinary and Holistic View)
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