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Omics and Systems Biology of Fungal Diseases
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Omics and Systems Biology of Fungal Diseases

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Pathogenesis and Disease Control".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 8675

Special Issue Editors

Dr. Chiung-Yu Hung

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Guest Editor
South Texas Center for Emerging Infectious Diseases, Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
Interests: fungal immunology; vaccine development host–pathogen interaction; coccidioidomcyosis; fungal virulence factors
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yufeng Wang

E-Mail Website
Guest Editor
South Texas Center for Emerging Infectious Diseases, Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
Interests: bioinformatics; systems biology; genomics; infectious diseases

Special Issue Information

Dear Colleagues,

Fungal pathogens have been and continue to be one of the major causes of infectious diseases in humans, animals, and plants, posing significant health, social, economic, and agricultural burdens. Combating fungal diseases requires a holistic understanding of the mechanisms underlying fungal pathogenesis, virulence, host–pathogen interactions, and drug resistance. Recent advances in high-throughput omics technologies and big data analytical approaches have set the stage for a quantum leap in our understanding of the biology of fungal pathogens and host–pathogen interactions for potential translational applications.

We welcome the submission of original research and review articles that focus on multidisciplinary omics (genomics, transcriptomics, proteomics, metabolomics, epigenomics) and systems biology approaches to the study of fungal diseases.

The potential topics include but are not limited to the following:

  • Molecular basis of infection and pathogenesis;
  • Virulence factors;
  • Host–pathogen interactions;
  • Host adaptation;
  • Host immune response;
  • Drug resistance;
  • Mycobiota;
  • Epidemiology;
  • Fungal secondary metabolites and diseases.

Prof. Dr. Chiung-Yu Hung
Prof. Dr. Yufeng Wang
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. Journal of Fungi 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 2600 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

  • Systems biology
  • Fungus
  • Infectious disease
  • Genomics
  • Proteomics
  • Metabolomics
  • Microbiome
  • Pathogenesis
  • Virulence
  • Host–pathogen interaction

Published Papers (4 papers)

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Research

14 pages, 4638 KiB  
Article
Development of an Imaging Flow Cytometry Method for Fungal Cytological Profiling and Its Potential Application in Antifungal Drug Development
by Courtney L. McMahon, Marisol Esqueda, Jieh-Juen Yu, Gina Wall, Jesus A. Romo, Taissa Vila, Ashok Chaturvedi, Jose L. Lopez-Ribot, Floyd Wormley and Chiung-Yu Hung
J. Fungi 2023, 9(7), 722; https://doi.org/10.3390/jof9070722 - 30 Jun 2023
Cited by 1 | Viewed by 1698
Abstract
Automated imaging techniques have been in increasing demand for the more advanced analysis and efficient characterization of cellular phenotypes. The success of the image-based profiling method hinges on assays that can rapidly and simultaneously capture a wide range of phenotypic features. We have [...] Read more.
Automated imaging techniques have been in increasing demand for the more advanced analysis and efficient characterization of cellular phenotypes. The success of the image-based profiling method hinges on assays that can rapidly and simultaneously capture a wide range of phenotypic features. We have developed an automated image acquisition method for fungal cytological profiling (FCP) using an imaging flow cytometer that can objectively measure over 250 features of a single fungal cell. Fungal cells were labeled with calcofluor white and FM4-64FX, which bind to the cell wall and lipophilic membrane, respectively. Images of single cells were analyzed using IDEAS® software. We first acquired FCPs of fungal cells treated with fluconazole, amphotericin B, and caspofungin, each with a distinct mode of action, to establish FCP databases of profiles associated with specific antifungal treatment. Once fully established, we investigated the potential application of this technique as a screening methodology to identify compounds with novel antifungal activity against Candida albicans and Cryptococcus neoformans. Altogether, we have developed a rapid, powerful, and novel image-profiling method for the phenotypic characterization of fungal cells, also with potential applications in antifungal drug development. Full article
(This article belongs to the Special Issue Omics and Systems Biology of Fungal Diseases)
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19 pages, 3695 KiB  
Article
Genomic Data Mining Reveals Abundant Uncharacterized Transporters in Coccidioides immitis and Coccidioides posadasii
by Hong Cai, Hao Zhang, Daniel H. Guo, Yufeng Wang and Jianying Gu
J. Fungi 2022, 8(10), 1064; https://doi.org/10.3390/jof8101064 - 10 Oct 2022
Viewed by 1264
Abstract
Coccidioides immitis and Coccidioides posadasii are causative agents of coccidioidomycosis, commonly known as Valley Fever. The increasing Valley Fever cases in the past decades, the expansion of endemic regions, and the rising azole drug-resistant strains have underscored an urgent need for a better [...] Read more.
Coccidioides immitis and Coccidioides posadasii are causative agents of coccidioidomycosis, commonly known as Valley Fever. The increasing Valley Fever cases in the past decades, the expansion of endemic regions, and the rising azole drug-resistant strains have underscored an urgent need for a better understanding of Coccidioides biology and new antifungal strategies. Transporters play essential roles in pathogen survival, growth, infection, and adaptation, and are considered as potential drug targets. However, the composition and roles of transport machinery in Coccidioides remain largely unknown. In this study, genomic data mining revealed an abundant, uncharacterized repertoire of transporters in Coccidioides genomes. The catalog included 1288 and 1235 transporter homologs in C. immitis and C. posadasii, respectively. They were further annotated to class, subclass, family, subfamily and range of substrates based on the Transport Classification (TC) system. They may play diverse roles in nutrient uptake, metabolite secretion, ion homeostasis, drug efflux, or signaling. This study represents an initial effort for a systems-level characterization of the transport machinery in these understudied fungal pathogens. Full article
(This article belongs to the Special Issue Omics and Systems Biology of Fungal Diseases)
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25 pages, 56155 KiB  
Article
Infection Process and Genome Assembly Provide Insights into the Pathogenic Mechanism of Destructive Mycoparasite Calcarisporium cordycipiticola with Host Specificity
by Qing Liu, Yanyan Xu, Xiaoling Zhang, Kuan Li, Xiao Li, Fen Wang, Fangxu Xu and Caihong Dong
J. Fungi 2021, 7(11), 918; https://doi.org/10.3390/jof7110918 - 28 Oct 2021
Cited by 9 | Viewed by 2748
Abstract
Calcarisporium cordycipiticola is the pathogen in the white mildew disease of Cordyceps militaris, one of the popular mushrooms. This disease frequently occurs and there is no effective method for disease prevention and control. In the present study, C. militaris is found to [...] Read more.
Calcarisporium cordycipiticola is the pathogen in the white mildew disease of Cordyceps militaris, one of the popular mushrooms. This disease frequently occurs and there is no effective method for disease prevention and control. In the present study, C. militaris is found to be the only host of C. cordycipiticola, indicating strict host specificity. The infection process was monitored by fluorescent labeling and scanning and transmission electron microscopes. C. cordycipiticola can invade into the gaps among hyphae of the fruiting bodies of the host and fill them gradually. It can degrade the hyphae of the host by both direct contact and noncontact. The parasitism is initially biotrophic, and then necrotrophic as mycoparasitic interaction progresses. The approximate chromosome-level genome assembly of C. cordycipiticola yielded an N50 length of 5.45 Mbp and a total size of 34.51 Mbp, encoding 10,443 proteins. Phylogenomic analysis revealed that C. cordycipiticola is phylogenetically close to its specific host, C. militaris. A comparative genomic analysis showed that the number of CAZymes of C. cordycipiticola was much less than in other mycoparasites, which might be attributed to its host specificity. Secondary metabolite cluster analysis disclosed the great biosynthetic capabilities and potential mycotoxin production capability. This study provides insights into the potential pathogenesis and interaction between mycoparasite and its host. Full article
(This article belongs to the Special Issue Omics and Systems Biology of Fungal Diseases)
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12 pages, 824 KiB  
Article
Genomic Diversity Analysis Reveals a Strong Population Structure in Histoplasma capsulatum LAmA (Histoplasma suramericanum)
by Fernando Almeida-Silva, Marcus de Melo Teixeira, Daniel R. Matute, Marcela de Faria Ferreira, Bridget M. Barker, Rodrigo Almeida-Paes, Allan J. Guimarães and Rosely M. Zancopé-Oliveira
J. Fungi 2021, 7(10), 865; https://doi.org/10.3390/jof7100865 - 15 Oct 2021
Cited by 8 | Viewed by 1915
Abstract
Histoplasmosis is a severe mycotic disease affecting thousands of immunocompetent and immunocompromised individuals with high incidence in Latin America, where the disease agents are Histoplasma capsulatum and Histoplasma suramericanum. In this work, we used whole-genome sequencing to infer the species diversity and [...] Read more.
Histoplasmosis is a severe mycotic disease affecting thousands of immunocompetent and immunocompromised individuals with high incidence in Latin America, where the disease agents are Histoplasma capsulatum and Histoplasma suramericanum. In this work, we used whole-genome sequencing to infer the species diversity and the population structure of H. suramericanum in South America. We find evidence for strong population structure and little admixture within the species. Genome-level phylogenetic trees indicate the existence of at least three different discrete populations. We recovered the existence of a previously identified population, LAmB, and confirm that it is highly differentiated along the whole genome. We also find that H. suramericanum is composed of two populations, one in Northern South America, and another in the southern portion of the continent. Moreover, one of the lineages from the southern population is endemic to Rio de Janeiro and there was no association with clinical data and species isolated from patients with histoplasmosis. Our results point out the need to characterize the symptomatology of histoplasmosis caused by different species and lineages of Histoplasma spp. Full article
(This article belongs to the Special Issue Omics and Systems Biology of Fungal Diseases)
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