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Xu D, Liu B, Wang J, Zhang Z. Bibliometric analysis of artificial intelligence for biotechnology and applied microbiology: Exploring research hotspots and frontiers. Front Bioeng Biotechnol 2022; 10:998298. [PMID: 36277390 PMCID: PMC9585160 DOI: 10.3389/fbioe.2022.998298] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background: In the biotechnology and applied microbiology sectors, artificial intelligence (AI) has been extensively used in disease diagnostics, drug research and development, functional genomics, biomarker recognition, and medical imaging diagnostics. In our study, from 2000 to 2021, science publications focusing on AI in biotechnology were reviewed, and quantitative, qualitative, and modeling analyses were performed. Methods: On 6 May 2022, the Web of Science Core Collection (WoSCC) was screened for AI applications in biotechnology and applied microbiology; 3,529 studies were identified between 2000 and 2022, and analyzed. The following information was collected: publication, country or region, references, knowledgebase, institution, keywords, journal name, and research hotspots, and examined using VOSviewer and CiteSpace V bibliometric platforms. Results: We showed that 128 countries published articles related to AI in biotechnology and applied microbiology; the United States had the most publications. In addition, 584 global institutions contributed to publications, with the Chinese Academy of Science publishing the most. Reference clusters from studies were categorized into ten headings: deep learning, prediction, support vector machines (SVM), object detection, feature representation, synthetic biology, amyloid, human microRNA precursors, systems biology, and single cell RNA-Sequencing. Research frontier keywords were represented by microRNA (2012–2020) and protein-protein interactions (PPIs) (2012–2020). Conclusion: We systematically, objectively, and comprehensively analyzed AI-related biotechnology and applied microbiology literature, and additionally, identified current hot spots and future trends in this area. Our review provides researchers with a comprehensive overview of the dynamic evolution of AI in biotechnology and applied microbiology and identifies future key research areas.
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Affiliation(s)
- Dongyu Xu
- Department of Computer, School of Intelligent Medicine, China Medical University, Shenyang, Liaoning, China
| | - Bing Liu
- Department of Bone Oncology, The People’s Hospital of Liaoning Province, Shenyang, Liaoning, China
| | - Jian Wang
- Department of Pathogenic Biology, School of Basic Medicine, China Medical University, Shenyang, Liaoning, China
| | - Zhichang Zhang
- Department of Computer, School of Intelligent Medicine, China Medical University, Shenyang, Liaoning, China
- *Correspondence: Zhichang Zhang,
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Alizadeh Z, Mahami-Oskouei M, Spotin A, Ahmadpour E, Cai P, Sandoghchian Shotorbani S, Pashazadeh F, Ansari F, Mohammadi H. MicroRNAs in helminth parasites: a systematic review. Curr Mol Med 2021; 22:779-808. [PMID: 34749620 DOI: 10.2174/1566524021666211108114009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/05/2021] [Accepted: 06/10/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) are about 22-nucleotide, small, non-coding RNAs that control gene expression post-transcriptionally. Helminth parasites usually express a unique repertoire of genes, including miRNAs, across different developmental stages with subtle regulatory mechanisms. OBJECTIVE There is a necessity to investigate the involvement of miRNAs in the development of parasites, host-parasite interaction, immune evasion and their abilities to govern infection in hosts. miRNAs present in helminth parasites have been summarized in the current systematic review (SR). METHODS Electronic databases, including PubMed, Scopus, ProQuest, Embase, and Google Scholar search engine, were searched to identify helminth miRNA studies published from February 1993 till December 2019. Only the published articles in English were included in the study. RESULTS A total of 1769 articles were preliminarily recorded. Following the strict inclusion and exclusion criteria, 105 studies were included in this SR. Most of these studies focused on the identification of miRNAs in helminth parasites and/or probing of differentially expressed host miRNA profiles in specific relevant tissues, while 12 studies aimed to detect parasite-derived miRNAs in host circulating system and 15 studies characterized extracellular vesicles (EV)-derived miRNAs secreted by parasites. CONCLUSION In the current SR, information regarding all miRNAs expressed in helminth parasites has been comprehensively provided and the utility of helminth parasites-derived miRNAs in diagnosis and control of parasitic infections has been discussed. Furthermore, functional studies on helminth-derived miRNAs have also been presented.
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Affiliation(s)
- Zahra Alizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Adel Spotin
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Ehsan Ahmadpour
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane. Australia
| | | | - Fariba Pashazadeh
- Research Center for Evidence-Based Medicine, Health Management and Safety Promotion Research Institute, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Fereshteh Ansari
- Research Center for Evidence-Based Medicine, Health Management and Safety Promotion Research Institute, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Hamed Mohammadi
- Non-Communicable Diseases Research Center, Alborz University of Medical Science, Karaj. Iran
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Kamenetzky L, Maldonado LL, Cucher MA. Cestodes in the genomic era. Parasitol Res 2021; 121:1077-1089. [PMID: 34665308 DOI: 10.1007/s00436-021-07346-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/10/2021] [Indexed: 12/20/2022]
Abstract
The first cestode genomes were obtained by an international consortium led by the Wellcome Sanger Institute that included representative institutions from countries where the sequenced parasites have been studied for decades, in part because they are etiological agents of endemic diseases (Argentina, Uruguay, Mexico, Canada, UK, Germany, Switzerland, Ireland, USA, Japan, and China). After this, several complete genomes were obtained reaching 16 species to date. Cestode genomes have smaller relative size compared to other animals including free-living flatworms. Moreover, the features genome size and repeat content seem to differ in the two analyzed orders. Cyclophyllidean species have smaller genomes and with fewer repetitive content than Diphyllobothriidean species. On average, cestode genomes have 13,753 genes with 6 exons per gene and 41% GC content. More than 5,000 shared cestode proteins were accurately annotated by the integration of gene predictions and transcriptome evidence being more than 40% of these proteins of unknown function. Several gene losses and reduction of gene families were found and could be related to the extreme parasitic lifestyle of these species. The application of cutting-edge sequencing technology allowed the characterization of the terminal sequences of chromosomes that possess unique characteristics. Here, we review the current status of knowledge of complete cestode genomes and place it within a comparative genomics perspective. Multidisciplinary work together with the implementation of new technologies will provide valuable information that can certainly improve our chances to finally eradicate or at least control diseases caused by cestodes.
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Affiliation(s)
- Laura Kamenetzky
- iB3, Instituto de Biociencias, Departamento de Fisiología Y Biología Molecular Y Celular, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Biotecnología y Biología traslacional, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
| | - Lucas L Maldonado
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Research On Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina
| | - Marcela A Cucher
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Research On Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina
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Faridi A, Mansouri M, Macchiaroli N, Afgar A, Mousavi SM, Rosenzvit MC, Harandi MF. MicroRNA profile of the strobilated worms of Echinococcus granulosus derived from in vivo and in vitro systems by using high-throughput approach. Parasitol Res 2021; 120:3203-3214. [PMID: 34351489 DOI: 10.1007/s00436-021-07251-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 07/13/2021] [Indexed: 11/26/2022]
Abstract
MicroRNAs are critical gene regulators at the post-transcriptional level and play essential roles in numerous developmental processes in metazoan parasites including the causative agent of cystic echinococcosis, Echinococcus granulosus. The molecular basis of different patterns of E. granulosus development in the canine definitive host and in in vitro culture systems is poorly understood. In the present study, miRNA transcriptomes of the strobilated worms derived from experimental infection in the definitive host were compared with those from diphasic culture system after 60-day protoscoleces cultivation. Total RNA was extracted from in vivo- and in vitro-derived strobilated worms. Small RNA libraries were constructed, and deep sequencing was performed. Subsequently, differential miRNA expressions and target predictions were obtained, and pathway analysis was performed by gene ontology and KEGG. Seven miRNAs were differentially expressed between the in vivo- and in vitro-derived worms. In addition, we reported 13 novel miRNA candidates and 42 conserved miRNAs. Four out of five top miRNAs with the highest read counts were shared between the in vivo and in vitro-derived worms, i.e., egr-miR-10a-5p, egr-let-7-5p, egr-bantam-3p, and egr-miR-71-5p. Target prediction of the differential miRNAs between the two systems showed significant differences in the membrane-enclosed lumen, membrane part, and an intrinsic component of the membrane. Findings of KEGG analysis indicated that differentially expressed miRNAs were involved in hippo, MAPK, and WNT signaling pathways. The study demonstrated a significant difference in miRNA transcriptomes and related signaling pathways between the two systems, suggesting the importance of host-parasite interplay in the fate of protoscoleces development in in vivo and in vitro systems.
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Affiliation(s)
- Ashkan Faridi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Natalia Macchiaroli
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología Y Parasitología Médica (IMPaM), Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Laboratorio de Genómica Y Bioinformática de Patógenos, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología Y Biología Molecular Y Celular, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Seyed Mohammad Mousavi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mara C Rosenzvit
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología Y Parasitología Médica (IMPaM), Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran.
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5
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Cucher MA, Ancarola ME, Kamenetzky L. The challenging world of extracellular RNAs of helminth parasites. Mol Immunol 2021; 134:150-160. [PMID: 33773158 DOI: 10.1016/j.molimm.2021.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/26/2021] [Accepted: 03/06/2021] [Indexed: 01/08/2023]
Abstract
In the last years, cell free or extracellular RNAs (ex-RNAs) have emerged as novel intercellular messengers between animal cells, including pathogens. In infectious diseases, ex-RNAs represent novel players in the host-pathogen and pathogen-pathogen interplays and have been described in parasitic helminths from the three major taxonomic groups: nematodes, trematodes and cestodes. Altogether, it is estimated that approximately 30 percent of the world's population is infected with helminths, which cause debilitating diseases and syndromes. Ex-RNAs are protected from degradation by encapsulation in extracellular vesicles (EV), or association to proteins or lipoproteins, and have been detected in the excretion/secretion products of helminth parasites, with EV as the preferred extracellular compartment under study. EV is the generic term used to describe a heterogenous group of subcellular membrane-bound particles, with varying sizes, biogenesis, density and composition. However, recent data suggests that this is not the only means used by helminth parasites to secrete RNAs since ex-RNAs can also be found in EV-depleted samples. Furthermore, the use of pathogen ex-RNAs as biomarkers promise the advent of new diagnostic tools though this field is still in early stages of exploration. In this review, we summarize current knowledge of vesicular and non-vesicular ex-RNAs secretion in helminth parasites, their potential as biomarkers and the evidence of their role in parasite and host reciprocal communication, together with unanswered questions in the field.
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Affiliation(s)
- Marcela A Cucher
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina; Institute of Research on Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina.
| | - María Eugenia Ancarola
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina; Institute of Research on Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina
| | - Laura Kamenetzky
- Laboratorio de Genómica y Bioinformática de Patógenos, iB3
- Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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Stegmayer G, Di Persia LE, Rubiolo M, Gerard M, Pividori M, Yones C, Bugnon LA, Rodriguez T, Raad J, Milone DH. Predicting novel microRNA: a comprehensive comparison of machine learning approaches. Brief Bioinform 2020; 20:1607-1620. [PMID: 29800232 DOI: 10.1093/bib/bby037] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 03/26/2018] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION The importance of microRNAs (miRNAs) is widely recognized in the community nowadays because these short segments of RNA can play several roles in almost all biological processes. The computational prediction of novel miRNAs involves training a classifier for identifying sequences having the highest chance of being precursors of miRNAs (pre-miRNAs). The big issue with this task is that well-known pre-miRNAs are usually few in comparison with the hundreds of thousands of candidate sequences in a genome, which results in high class imbalance. This imbalance has a strong influence on most standard classifiers, and if not properly addressed in the model and the experiments, not only performance reported can be completely unrealistic but also the classifier will not be able to work properly for pre-miRNA prediction. Besides, another important issue is that for most of the machine learning (ML) approaches already used (supervised methods), it is necessary to have both positive and negative examples. The selection of positive examples is straightforward (well-known pre-miRNAs). However, it is difficult to build a representative set of negative examples because they should be sequences with hairpin structure that do not contain a pre-miRNA. RESULTS This review provides a comprehensive study and comparative assessment of methods from these two ML approaches for dealing with the prediction of novel pre-miRNAs: supervised and unsupervised training. We present and analyze the ML proposals that have appeared during the past 10 years in literature. They have been compared in several prediction tasks involving two model genomes and increasing imbalance levels. This work provides a review of existing ML approaches for pre-miRNA prediction and fair comparisons of the classifiers with same features and data sets, instead of just a revision of published software tools. The results and the discussion can help the community to select the most adequate bioinformatics approach according to the prediction task at hand. The comparative results obtained suggest that from low to mid-imbalance levels between classes, supervised methods can be the best. However, at very high imbalance levels, closer to real case scenarios, models including unsupervised and deep learning can provide better performance.
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Affiliation(s)
- Georgina Stegmayer
- sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - Leandro E Di Persia
- sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - Mariano Rubiolo
- sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - Matias Gerard
- sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - Milton Pividori
- sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - Cristian Yones
- sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - Leandro A Bugnon
- sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - Tadeo Rodriguez
- sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - Jonathan Raad
- sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - Diego H Milone
- sinc(i), Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
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7
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He Z, Yan T, Yuan Y, Yang D, Yang G. miRNAs and lncRNAs in Echinococcus and Echinococcosis. Int J Mol Sci 2020; 21:ijms21030730. [PMID: 31979099 PMCID: PMC7037763 DOI: 10.3390/ijms21030730] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/16/2020] [Accepted: 01/19/2020] [Indexed: 01/04/2023] Open
Abstract
Echinococcosis are considered to be potentially lethal zoonotic diseases that cause serious damage to hosts. The metacestode of Echinococcus multilocularis and E. granulosus can result in causing the alveolar and cystic echinococcoses, respectively. Recent studies have shown that non-coding RNAs are widely expressed in Echinococcus spp. and hosts. In this review, the two main types of non-coding RNAs—long non-coding RNAs (lncRNAs) and microRNAs (miRNAs)—and the wide-scale involvement of these molecules in these parasites and their hosts were discussed. The expression pattern of miRNAs in Echinococcus spp. is species- and developmental stage-specific. Furthermore, common miRNAs were detected in three Echinococcus spp. and their intermediate hosts. Here, we primarily focus on recent insights from transcriptome studies, the expression patterns of miRNAs and lncRNAs, and miRNA-related databases and techniques that are used to investigate miRNAs in Echinococcus and echinococcosis. This review provides new avenues for screening therapeutic and diagnostic markers.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
| | - Ya Yuan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Correspondence: ; Tel.: +86-028-8278-3043
| | - Guangyou Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China;
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8
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Macchiaroli N, Cucher M, Kamenetzky L, Yones C, Bugnon L, Berriman M, Olson PD, Rosenzvit MC. Identification and expression profiling of microRNAs in Hymenolepis. Int J Parasitol 2019; 49:211-223. [PMID: 30677390 DOI: 10.1016/j.ijpara.2018.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 02/08/2023]
Abstract
Tapeworms (cestodes) of the genus Hymenolepis are the causative agents of hymenolepiasis, a neglected zoonotic disease. Hymenolepis nana is the most prevalent human tapeworm, especially affecting children. The genomes of Hymenolepis microstoma and H. nana have been recently sequenced and assembled. MicroRNAs (miRNAs), a class of small non-coding RNAs, are principle regulators of gene expression at the post-transcriptional level and are involved in many different biological processes. In previous work, we experimentally identified miRNA genes in the cestodes Echinococcus, Taenia and Mesocestoides. However, current knowledge about miRNAs in Hymenolepis is limited. In this work we described for the first known time the expression profile of the miRNA complement in H. microstoma, and discovered miRNAs in H. nana. We found a reduced complement of 37 evolutionarily conserved miRNAs, putatively reflecting their low morphological complexity and parasitic lifestyle. We found high expression of a few miRNAs in the larval stage of H. microstoma that are conserved in other cestodes, suggesting that these miRNAs may have important roles in development, survival and for host-parasite interplay. We performed a comparative analysis of the identified miRNAs across the Cestoda and showed that most of the miRNAs in Hymenolepis are located in intergenic regions, implying that they are independently transcribed. We found a Hymenolepis-specific cluster composed of three members of the mir-36 family. Also, we found that one of the neighboring genes of mir-10 was a Hox gene as in most bilaterial species. This study provides a valuable resource for further experimental research in cestode biology that might lead to improved detection and control of these neglected parasites. The comprehensive identification and expression analysis of Hymenolepis miRNAs can help to identify novel biomarkers for diagnosis and/or novel therapeutic targets for the control of hymenolepiasis.
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Affiliation(s)
- Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Marcela Cucher
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence, (sinc(i)), FICH-UNL-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Santa Fe, Argentina
| | - Leandro Bugnon
- Research Institute for Signals, Systems and Computational Intelligence, (sinc(i)), FICH-UNL-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Santa Fe, Argentina
| | - Matt Berriman
- Parasite Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter D Olson
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Mara Cecilia Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina.
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Palevich N, Britton C, Kamenetzky L, Mitreva M, de Moraes Mourão M, Bennuru S, Quack T, Scholte LLS, Tyagi R, Slatko BE. Tackling Hypotheticals in Helminth Genomes. Trends Parasitol 2018; 34:179-183. [PMID: 29249363 PMCID: PMC11021132 DOI: 10.1016/j.pt.2017.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/12/2017] [Accepted: 11/22/2017] [Indexed: 11/25/2022]
Abstract
Advancements in genome sequencing have led to the rapid accumulation of uncharacterized 'hypothetical proteins' in the public databases. Here we provide a community perspective and some best-practice approaches for the accurate functional annotation of uncharacterized genomic sequences.
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Affiliation(s)
- Nikola Palevich
- Molecular Parasitology, Animal Science, AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand.
| | - Collette Britton
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, UK
| | - Laura Kamenetzky
- Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM-UBA-CONICET), Buenos Aires, Argentina
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA; Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | | | | | - Thomas Quack
- BFS, Institute of Parasitology, Justus Liebig University Giessen, Germany
| | | | - Rahul Tyagi
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Barton E Slatko
- Molecular Parasitology Division, New England Biolabs, Inc., Ipswich, MA, USA
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10
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Pérez MG, Macchiaroli N, Lichtenstein G, Conti G, Asurmendi S, Milone DH, Stegmayer G, Kamenetzky L, Cucher M, Rosenzvit MC. microRNA analysis of Taenia crassiceps cysticerci under praziquantel treatment and genome-wide identification of Taenia solium miRNAs. Int J Parasitol 2017; 47:643-653. [DOI: 10.1016/j.ijpara.2017.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 12/14/2022]
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11
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Arora N, Tripathi S, Singh AK, Mondal P, Mishra A, Prasad A. Micromanagement of Immune System: Role of miRNAs in Helminthic Infections. Front Microbiol 2017; 8:586. [PMID: 28450853 PMCID: PMC5390025 DOI: 10.3389/fmicb.2017.00586] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/21/2017] [Indexed: 01/09/2023] Open
Abstract
Helminthic infections fall under neglected tropical diseases, although they inflict severe morbidity to human and causes major economic burden on health care system in many developing countries. There is increased effort to understand their immunopathology in recent days due to their immuno-modulatory capabilities. Immune response is primarily controlled at the transcriptional level, however, microRNA-mediated RNA interference is emerging as important regulatory machinery that works at the translation level. In the past decade, microRNA (miRNA/miR) research has advanced with significant momentum. The result is ever increasing list of curated sequences from a broad panel of organisms including helminths. Several miRNAs had been discovered from trematodes, nematodes and cestodes like let-7, miR155, miR-199, miR-134, miR-223, miR-146, and fhe-mir-125a etc., with potential role in immune modulation. These miRs had been associated with TGF-β, MAPK, Toll-like receptor, PI3K/AKT signaling pathways and insulin growth factor regulation. Thus, controlling the immune cells development, survival, proliferation and death. Apart from micromanagement of immune system, they also express certain unique miRNA also like cis-miR-001, cis-miR-2, cis-miR-6, cis-miR-10, cis-miR-18, cis-miR-19, trs-mir-0001, fhe-miR-01, fhe-miR-07, fhe-miR-08, egr-miR-4988, egr-miR-4989 etc. The specific role played by most of these species specific unique miRs are yet to be discovered. However, these newly discovered miRNAs might serve as novel targets for therapeutic intervention or biomarkers for parasitic infections.
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Affiliation(s)
- Naina Arora
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
| | - Shweta Tripathi
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
| | - Aloukick K Singh
- Department of Immunology, Weizmann Institute of ScienceRehovot, Israel
| | - Prosenjit Mondal
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
| | - Amit Prasad
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
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