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Parasite Omics: Applications, Tools and Databases
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Parasite Omics: Applications, Tools and Databases

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 April 2022) | Viewed by 15247

Special Issue Editors

Prof. Dr. Petrus Tang

E-Mail Website
Guest Editor
Department of Parasitology/Bioinformatice Core Laboratory, Chang Gung University, Taoyuan City 33302, Taiwan
Interests: genomics; transcriptomics; proteomics; bioinformatics and computational biology
Prof. Dr. Wei Hu

E-Mail Website
Guest Editor
1. Department of Microbiology and Immunology, School of Life Sciences, Fudan University, Shanghai, China
2. School of Life Sciences, Inner Mongolia University, Hohhot, China
Interests: infectious diseases; genomics

Special Issue Information

Dear Colleagues, 

Recent advances in a series of high-throughput “-omics” technologies allow the simultaneous examination of thousands of genes, transcripts, proteins, and metabolites with high-throughput techniques and analytical tools to extract information. These technological breakthroughs and data-driven research models have improved our knowledge and understanding of parasitic diseases at the molecular level. One of the bottlenecks is integrating multi-omics data from different sources to explore important research areas such as drug resistance, unique/unknown genes, host–parasite interactions, parasitism, and disease pathogenesis at a systemic level.

The goal of this Special Issue, dedicated to "Parasite Omics: Applications, Tools, and Databases," is to publish high-quality manuscripts with special emphasis on using omics approaches to study parasitic diseases. We welcome reviews, new methods, bioinformatics tools, databases, short communications, and original articles discussing recent advances and developments in the field of parasite omics.

We look forward to your contributions.

Prof. Dr. Petrus Tang
Prof. Dr. Wei Hu
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. Genes 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.

Published Papers (6 papers)

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Research

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15 pages, 1991 KiB  
Article
Exploiting Comparative Omics to Understand the Pathogenic and Virulence-Associated Protease: Anti-Protease Relationships in the Zoonotic Parasites Fasciola hepatica and Fasciola gigantica
by Krystyna Cwiklinski and John Pius Dalton
Genes 2022, 13(10), 1854; https://doi.org/10.3390/genes13101854 - 14 Oct 2022
Cited by 6 | Viewed by 2440
Abstract
The helminth parasites, Fasciola hepatica and Fasciola gigantica, are the causative agents of fasciolosis, a global and economically important disease of people and their livestock. Proteases are pivotal to an array of biological processes related to parasitism (development, feeding, immune evasion, virulence) [...] Read more.
The helminth parasites, Fasciola hepatica and Fasciola gigantica, are the causative agents of fasciolosis, a global and economically important disease of people and their livestock. Proteases are pivotal to an array of biological processes related to parasitism (development, feeding, immune evasion, virulence) and therefore their action requires strict regulation by parasite anti-proteases (protease inhibitors). By interrogating the current publicly available Fasciola spp. large sequencing datasets, including several genome assemblies and life cycle stage-specific transcriptome and proteome datasets, we reveal the complex profile and structure of proteases and anti-proteases families operating at various stages of the parasite’s life cycle. Moreover, we have discovered distinct profiles of peptidases and their cognate inhibitors expressed by the parasite stages in the intermediate snail host, reflecting the different environmental niches in which they move, develop and extract nutrients. Comparative genomics revealed a similar cohort of peptidase inhibitors in F. hepatica and F. gigantica but a surprisingly reduced number of cathepsin peptidases genes in the F. gigantica genome assemblies. Chromosomal location of the F. gigantica genes provides new insights into the evolution of these gene families, and critical data for the future analysis and interrogation of Fasciola spp. hybrids spreading throughout the Asian and African continents. Full article
(This article belongs to the Special Issue Parasite Omics: Applications, Tools and Databases)
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23 pages, 4490 KiB  
Article
Omics Analyses of Trichomonas vaginalis Actin and Tubulin and Their Participation in Intercellular Interactions and Cytokinesis
by Sebastián Lorenzo-Benito, Luis Alberto Rivera-Rivas, Lizbeth Sánchez-Ayala, Jaime Ortega-López, Octavio Montes-Flores, Daniel Talamás-Lara and Rossana Arroyo
Genes 2022, 13(6), 1067; https://doi.org/10.3390/genes13061067 - 15 Jun 2022
Cited by 3 | Viewed by 2639
Abstract
Actin and tubulin proteins from Trichomonas vaginalis are crucial for morphogenesis and mitosis. This parasite has 10 and 11 genes coding bonafide actin and tubulin proteins, respectively. Hence, the goal of this work was to analyze these actin and tubulin genes, their expression [...] Read more.
Actin and tubulin proteins from Trichomonas vaginalis are crucial for morphogenesis and mitosis. This parasite has 10 and 11 genes coding bonafide actin and tubulin proteins, respectively. Hence, the goal of this work was to analyze these actin and tubulin genes, their expression at the mRNA and protein levels, and their parasite localization in intercellular interaction and cytokinesis. Representative bonafide actin (tvact1) and tubulin (tvtubα1) genes were cloned into and expressed in Escherichia coli. The recombinant proteins TvACT1r and TvTUBα1r were affinity purified and used as antigens to produce polyclonal antibodies. These antibodies were used in 1DE and 2DE WB and indirect immunofluorescence assays (IFA). By IFA, actin was detected as a ring on the periphery of ameboid, ovoid, and cold-induced cyst-like parasites, on pseudopods of amoeboid parasites, and in cytoplasmic extensions (filopodia) in cell–cell interactions. Tubulin was detected in the axostyle, flagellum, undulating membrane, and paradesmose during mitosis. Paradesmose was observed by IFA mainly during cytokinesis. By scanning electron microscopy, a tubulin-containing nanotubular structure similar to the tunneling nanotubes (TNTs) was also detected in the last stage of cytokinesis. In conclusion, actin and tubulin are multigene families differentially expressed that play important roles in intercellular interactions and cytokinesis. Full article
(This article belongs to the Special Issue Parasite Omics: Applications, Tools and Databases)
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11 pages, 1392 KiB  
Article
Identification of Endosymbiotic Virus in Small Extracellular Vesicles Derived from Trichomonas vaginalis
by Seow-Chin Ong, Wei-Hung Cheng, Fu-Man Ku, Chih-Yu Tsai, Po-Jung Huang, Chi-Ching Lee, Yuan-Ming Yeh, Petr Rada, Ivan Hrdý, Ravi Kumar Narayanasamy, Tamara Smutná, Rose Lin, Hong-Wei Luo, Cheng-Hsun Chiu, Jan Tachezy and Petrus Tang
Genes 2022, 13(3), 531; https://doi.org/10.3390/genes13030531 - 17 Mar 2022
Cited by 6 | Viewed by 2836
Abstract
Accumulated evidence suggests that the endosymbiotic Trichomonasvirus (TVV) may play a role in the pathogenesis and drug susceptibility of Trichomonas vaginalis. Several reports have shown that extracellular vesicles (EVs) released from TVV-positive (TVV+) trichomonads can modulate the immune response in human vaginal [...] Read more.
Accumulated evidence suggests that the endosymbiotic Trichomonasvirus (TVV) may play a role in the pathogenesis and drug susceptibility of Trichomonas vaginalis. Several reports have shown that extracellular vesicles (EVs) released from TVV-positive (TVV+) trichomonads can modulate the immune response in human vaginal epithelial cells and animal models. These results prompted us to examine whether EVs released from TVV+ isolates contained TVV. We isolated small extracellular vesicles (sEVs) from six T. vaginalis isolates that were either TVV free (ATCC 50143), harbored a single (ATCC 30236, ATCC 30238, T1), two (ATCC PRA-98), or three TVV subspecies (ATCC 50148). The presence of TVV subspecies in the six isolates was observed using reverse transcription-polymerase chain reaction (RT-PCR). Transmission electron microscopy (TEM) confirmed the presence of cup-shaped sEVs with a size range from 30–150 nm. Trichomonas vaginalis tetraspanin (TvTSP1; TVAG_019180), the classical exosome marker, was identified in all the sEV preparations. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that all the sEVs isolated from TVV+ isolates contain viral capsid proteins derived from the same TVV subspecies in that isolate as demonstrated by RT-PCR. To provide more comprehensive information on the TVV subspecies population in other T. vaginalis isolates, we investigated the distribution of TVV subspecies in twenty-four isolates by mining the New-Generation Sequencing (NGS) RNAseq datasets. Our results should be beneficial for future studies investigating the role of TVV on the pathogenicity of T. vaginalis and the possible transmission of virus subspecies among different isolates via sEVs. Full article
(This article belongs to the Special Issue Parasite Omics: Applications, Tools and Databases)
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19 pages, 3986 KiB  
Article
Genetic Polymorphism and Natural Selection of Apical Membrane Antigen-1 in Plasmodium falciparum Isolates from Vietnam
by Jung-Mi Kang, Hương Giang Lê, Tuấn Cường Võ, Haung Naw, Won Gi Yoo, Woon-Mok Sohn, Nguyen Thi Minh Trinh, Huynh-Hong Quang and Byoung-Kuk Na
Genes 2021, 12(12), 1903; https://doi.org/10.3390/genes12121903 - 27 Nov 2021
Cited by 4 | Viewed by 2138
Abstract
Apical membrane antigen-1 of Plasmodium falciparum (PfAMA-1) is a leading malaria vaccine candidate antigen. However, the genetic diversity of pfama-1 and associated antigenic variation in global P. falciparum field isolates are major hurdles to the design of an efficacious vaccine formulated with this [...] Read more.
Apical membrane antigen-1 of Plasmodium falciparum (PfAMA-1) is a leading malaria vaccine candidate antigen. However, the genetic diversity of pfama-1 and associated antigenic variation in global P. falciparum field isolates are major hurdles to the design of an efficacious vaccine formulated with this antigen. Here, we analyzed the genetic structure and the natural selection of pfama-1 in the P. falciparum population of Vietnam. A total of 37 distinct haplotypes were found in 131 P. falciparum Vietnamese isolates. Most amino acid changes detected in Vietnamese pfama-1 were localized in the ectodomain, domains I, II, and III. Overall patterns of major amino acid changes in Vietnamese pfama-1 were similar to those of global pfama-1, but the frequencies of the amino acid changes slightly differed by country. Novel amino acid changes were also identified in Vietnamese pfama-1. Vietnamese pfama-1 revealed relatively lower genetic diversity than currently analyzed pfama-1 in other geographical regions, and suggested a distinct genetic differentiation pattern. Evidence for natural selection was detected in Vietnamese pfama-1, but it showed purifying selection unlike the global pfama-1 analyzed so far. Recombination events were also found in Vietnamese pfama-1. Major amino acid changes that were commonly identified in global pfama-1 were mainly localized to predicted B-cell epitopes, RBC-binding sites, and IUR regions. These results provide important information for understanding the genetic nature of the Vietnamese pfama-1 population, and have significant implications for the design of a vaccine based on PfAMA-1. Full article
(This article belongs to the Special Issue Parasite Omics: Applications, Tools and Databases)
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14 pages, 3481 KiB  
Article
Identification and Expression Profiling of Circulating MicroRNAs in Serum of Cysticercus pisiformis-Infected Rabbits
by Guoliang Chen, Liqun Wang, Tingli Liu, Yanping Li, Shaohua Zhang, Hong Li and Xuenong Luo
Genes 2021, 12(10), 1591; https://doi.org/10.3390/genes12101591 - 9 Oct 2021
Cited by 7 | Viewed by 1902
Abstract
Cysticercus pisiformis (C. pisiformis), the larval form of Taenia pisiformis, parasitize mainly the liver, omentum and mesentery of rabbits and cause huge economic losses in the rabbit breeding industry. MicroRNA (miRNA), a short non-coding RNA, is widely and stably distributed [...] Read more.
Cysticercus pisiformis (C. pisiformis), the larval form of Taenia pisiformis, parasitize mainly the liver, omentum and mesentery of rabbits and cause huge economic losses in the rabbit breeding industry. MicroRNA (miRNA), a short non-coding RNA, is widely and stably distributed in the plasma and serum. Numerous data demonstrates that, after parasitic infection, miRNAs become the key regulatory factor for controlling host biological processes. However, the roles of serum miRNAs in C. pisiformis-infected rabbits have not been elucidated. In this study, we compared miRNA expression profiles between the C. pisiformis-infected and healthy rabbit serum using RNA-seq. A total of 192 miRNAs were differentially expressed (fold change ≥ 2 and p < 0.05), including 79 up- and 113 downregulated miRNAs. These data were verified by qRT-PCR (real time quantitative polymerase chain reaction) analysis. Additionally, GO analysis showed that the target genes of these dysregulated miRNAs were most enriched in cellular, single-organism and metabolic processes. KEGG pathway analysis showed that these miRNAs target genes were involved in PI3K-Akt, viral carcinogenesis and B cell receptor signaling pathways. Interestingly, after aligning clean reads to the T. pisiformis genome, four (miR-124-3p_3, miR-124-3p_4, miR-124a and novel-miR1) T. pisiformis-derived miRNAs were found. Of these, novel-miR1was upregulated in different periods after C. pisiformis infection, which was verified qRT-PCR, and pre- novel-miR-1 was amplified from the cysticerci by RT-PCR, implying novel-miR-1 was derived from C. pisiformis and has great potential for the diagnosis of Cysticercosis pisiformis infection. This is the first investigation of miRNA expression profile and function in the serum of rabbits infected by C. pisiformis, providing fundamental data for developing diagnostic targets for Cysticercosis pisiformis. Full article
(This article belongs to the Special Issue Parasite Omics: Applications, Tools and Databases)
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Review

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11 pages, 576 KiB  
Review
Molecular Dissection of Phagocytosis by Proteomic Analysis in Entamoeba histolytica
by Natsuki Watanabe, Kumiko Nakada-Tsukui and Tomoyoshi Nozaki
Genes 2023, 14(2), 379; https://doi.org/10.3390/genes14020379 - 31 Jan 2023
Cited by 2 | Viewed by 1782
Abstract
Entamoeba histolytica is the enteric protozoan parasite responsible for amebiasis. Trophozoites of E. histolytica ingest human cells in the intestine and other organs, which is the hallmark of its pathogenesis. Phagocytosis and trogocytosis are pivotal biological functions for its virulence and also contribute [...] Read more.
Entamoeba histolytica is the enteric protozoan parasite responsible for amebiasis. Trophozoites of E. histolytica ingest human cells in the intestine and other organs, which is the hallmark of its pathogenesis. Phagocytosis and trogocytosis are pivotal biological functions for its virulence and also contribute to the proliferation of nutrient uptake from the environment. We previously elucidated the role of a variety of proteins associated with phagocytosis and trogocytosis, including Rab small GTPases, Rab effectors, including retromer, phosphoinositide-binding proteins, lysosomal hydrolase receptors, protein kinases, and cytoskeletal proteins. However, a number of proteins involved in phagocytosis and trogocytosis remain to be identified, and mechanistic details of their involvement must be elucidated at the molecular level. To date, a number of studies in which a repertoire of proteins associated with phagosomes and potentially involved in phagocytosis have been conducted. In this review, we revisited all phagosome proteome studies we previously conducted in order to reiterate information on the proteome of phagosomes. We demonstrated the core set of constitutive phagosomal proteins and also the set of phagosomal proteins recruited only transiently or in condition-dependent fashions. The catalogs of phagosome proteomes resulting from such analyses can be a useful source of information for future mechanistic studies as well as for confirming or excluding a possibility of whether a protein of interest in various investigations is likely or is potentially involved in phagocytosis and phagosome biogenesis. Full article
(This article belongs to the Special Issue Parasite Omics: Applications, Tools and Databases)
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