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Valldeperes M, Yerro PP, López-Olvera JR, Fandos P, Lavín S, Escofet RCS, Mentaberre G, León FJCM, Espinosa J, Ráez-Bravo A, Pérez JM, Tampach S, Estruch J, Velarde R, Granados JE. Diseases of Iberian ibex ( Capra pyrenaica). EUR J WILDLIFE RES 2023; 69:63. [PMID: 37274486 PMCID: PMC10233571 DOI: 10.1007/s10344-023-01684-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/03/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023]
Abstract
Iberian ibex (Capra pyrenaica) is an ecologically and economically relevant medium-sized emblematic mountain ungulate. Diseases participate in the population dynamics of the species as a regulating agent, but can also threaten the conservation and viability of vulnerable population units. Moreover, Iberian ibex can also be a carrier or even a reservoir of pathogens shared with domestic animals and/or humans, being therefore a concern for livestock and public health. The objective of this review is to compile the currently available knowledge on (1) diseases of Iberian ibex, presented according to their relevance on the health and demography of free-ranging populations; (2) diseases subjected to heath surveillance plans; (3) other diseases reported in the species; and (4) diseases with particular relevance in captive Iberian ibex populations. The systematic review of all the information on diseases affecting the species unveils unpublished reports, scientific communications in meetings, and scientific articles, allowing the first comprehensive compilation of Iberian ibex diseases. This review identifies the gaps in knowledge regarding pathogenesis, immune response, diagnostic methods, treatment, and management of diseases in Iberian ibex, providing a base for future research. Moreover, this challenges wildlife and livestock disease and wildlife population managers to assess the priorities and policies currently implemented in Iberian ibex health surveillance and monitoring and disease management.
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Affiliation(s)
- Marta Valldeperes
- Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193 Barcelona, Bellaterra Spain
- Wildlife Ecology & Health Group (WE&H), Barcelona, Spain
| | - Paloma Prieto Yerro
- Parque Natural de las Sierras de Cazorla, Segura y Las Villas, C/ Martínez Falero 11, 23470 Cazorla Jaén, Spain
- Grupo de Investigación RNM 118. Biología de Especies Cinegéticas y Plagas, Jaén, Spain
| | - Jorge Ramón López-Olvera
- Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193 Barcelona, Bellaterra Spain
- Wildlife Ecology & Health Group (WE&H), Barcelona, Spain
| | | | - Santiago Lavín
- Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193 Barcelona, Bellaterra Spain
- Wildlife Ecology & Health Group (WE&H), Barcelona, Spain
| | | | - Gregorio Mentaberre
- Wildlife Ecology & Health Group (WE&H), Barcelona, Spain
- Departament de Ciència Animal, Universitat de Lleida, 25198 Lleida, Spain
| | | | - José Espinosa
- Departamento de Sanidad Animal, Facultad de Veterinaria and Instituto de Ganadería de Montaña (CSIC-ULE), Universidad de León, 24071 León, Spain
| | - Arián Ráez-Bravo
- Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193 Barcelona, Bellaterra Spain
- Wildlife Ecology & Health Group (WE&H), Barcelona, Spain
| | - Jesús M. Pérez
- Wildlife Ecology & Health Group (WE&H), Barcelona, Spain
- Grupo de Investigación RNM 118. Biología de Especies Cinegéticas y Plagas, Jaén, Spain
- Department of Animal and Plant Biology, and Ecology, Jaén University, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Stefania Tampach
- Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193 Barcelona, Bellaterra Spain
- Wildlife Ecology & Health Group (WE&H), Barcelona, Spain
| | - Josep Estruch
- Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193 Barcelona, Bellaterra Spain
- Wildlife Ecology & Health Group (WE&H), Barcelona, Spain
| | - Roser Velarde
- Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Universitat Autònoma de Barcelona, 08193 Barcelona, Bellaterra Spain
- Wildlife Ecology & Health Group (WE&H), Barcelona, Spain
| | - José Enrique Granados
- Wildlife Ecology & Health Group (WE&H), Barcelona, Spain
- Grupo de Investigación RNM 118. Biología de Especies Cinegéticas y Plagas, Jaén, Spain
- Parque Nacional y Parque Natural de Sierra Nevada. Ctra., Antigua de Sierra Nevada Km 7, Pinos Genil, 18191 Granada, Spain
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Wang T, Gasser RB, Korhonen PK, Young ND, Ang CS, Williamson NA, Ma G, Samarawickrama GR, Fernando DD, Fischer K. Proteomic analysis of Sarcoptes scabiei reveals that proteins differentially expressed between eggs and female adult stages are involved predominantly in genetic information processing, metabolism and/or host-parasite interactions. PLoS Negl Trop Dis 2022; 16:e0010946. [PMID: 36472966 PMCID: PMC9725168 DOI: 10.1371/journal.pntd.0010946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Presently, there is a dearth of proteomic data for parasitic mites and their relationship with the host animals. Here, using a high throughput LC-MS/MS-based approach, we undertook the first comprehensive, large-scale proteomic investigation of egg and adult female stages of the scabies mite, Sarcoptes scabiei-one of the most important parasitic mites of humans and other animals worldwide. In total, 1,761 S. scabiei proteins were identified and quantified with high confidence. Bioinformatic analyses revealed differentially expressed proteins to be involved predominantly in biological pathways or processes including genetic information processing, energy (oxidative phosphorylation), nucleotide, amino acid, carbohydrate and/or lipid metabolism, and some adaptive processes. Selected, constitutively and highly expressed proteins, such as peptidases, scabies mite inactivated protease paralogues (SMIPPs) and muscle proteins (myosin and troponin), are proposed to be involved in key biological processes within S. scabiei, host-parasite interactions and/or the pathogenesis of scabies. These proteomic data will enable future molecular, biochemical and physiological investigations of early developmental stages of S. scabiei and the discovery of novel interventions, targeting the egg stage, given its non-susceptibility to acaricides currently approved for the treatment of scabies in humans.
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Affiliation(s)
- Tao Wang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
- * E-mail:
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Australia
| | - Nicholas A. Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Australia
| | - Guangxu Ma
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Gangi R. Samarawickrama
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Veterinary Science, University of Queensland, Gatton, Australia
| | - Deepani D. Fernando
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Katja Fischer
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
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Abdelaziz E, Elbahy N, El-Bahrawy A, ElKhatam A, AbouLaila M. Prevalence, hematological, serum biochemical, histopathology, and molecular characterization of Sarcoptes scabiei in naturally infected rabbits from Minoufiya Governorate, Egypt. Vet Parasitol Reg Stud Reports 2022; 36:100788. [PMID: 36436899 DOI: 10.1016/j.vprsr.2022.100788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 09/07/2022] [Accepted: 09/27/2022] [Indexed: 01/14/2023]
Abstract
Sarcoptic mange is a highly contagious ectoparasitic disease that causes significant economic losses in the rabbit industry. The current study intended to reveal the infection rate, histopathology, and genetic characterization of Sarcoptes scabiei (S. scabiei) in naturally infected rabbits in Minoufiya governorate, Egypt. A total of 1120 rabbits were physically inspected for sarcoptic mange lesions and infections were confirmed microscopically. In addition, the various hematologic and serum biochemical parameters in naturally infected and non-infected rabbits were evaluated. A histopathological examination was performed. Genomic DNA was isolated from skin scraping samples and amplified using PCR primers targeting the ITS-2 region and Cox1 and Actin genes, which were then sequenced and phylogenetically analyzed. The overall prevalence of S. scabiei was 5.98%. Although the infection was higher in females than males, the analysis showed no statistically significant difference. White blood cells, lymphocytes, liver enzymes (GOT and GPT), urea, total antioxidant capacity, glutathione peroxidase, and malondialdehyde dramatically increased whereas RBCs, Hb, and MCV significantly decreased. There were epidermal thickening and hyperkeratosis, inflammation, and homogenous faint pink edematous lesions, and the S. scabiei was attached to the stratum corneum and/or burrowing through it, causing tunnels. PCR and sequence analysis of the ITS-2 region and Cox1 and Actin genes showed that the sequences in the present study were highly identical to the homologous sequences from several countries and confirmed that the mite was S. scabiei. This study presented the first molecular characterization of S. scabiei in rabbits from Minoufiya Governorate, Egypt.
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Korhonen PK, Wang T, Young ND, Samarawickrama GR, Fernando DD, Ma G, Gasser RB, Fischer K. Evidence that Transcriptional Alterations in Sarcoptes scabiei Are under Tight Post-Transcriptional (microRNA) Control. Int J Mol Sci 2022; 23:9719. [PMID: 36077116 PMCID: PMC9456212 DOI: 10.3390/ijms23179719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Here, we explored transcriptomic differences among early egg (Ee), late egg (Le) and adult female (Af) stages of the scabies mite, Sarcoptes scabiei, using an integrative bioinformatic approach. We recorded a high, negative correlation between miRNAs and genes with decreased mRNA transcription between the developmental stages, indicating substantial post-transcriptional repression; we also showed a positive correlation between miRNAs and genes with increased mRNA transcription, suggesting indirect post-transcriptional regulation. The alterations in mRNA transcription between the egg and adult female stages of S. scabiei were inferred to be linked to metabolism (including carbohydrate and lipid degradation, amino acid and energy metabolism), environmental information processing (e.g., signal transduction and signalling molecules), genetic information processing (e.g., transcription and translation) and/or organismal systems. Taken together, these results provide insight into the transcription of this socioeconomically important parasitic mite, with a particular focus on the egg stage. This work encourages further, detailed laboratory studies of miRNA regulation across all developmental stages of S. scabiei and might assist in discovering new intervention targets in the egg stage of S. scabiei.
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Fernando DD, Korhonen PK, Gasser RB, Fischer K. An RNA Interference Tool to Silence Genes in Sarcoptes scabiei Eggs. Int J Mol Sci 2022; 23:ijms23020873. [PMID: 35055058 PMCID: PMC8777771 DOI: 10.3390/ijms23020873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/10/2022] Open
Abstract
In a quest for new interventions against scabies-a highly significant skin disease of mammals, caused by a parasitic mite Sarcoptes scabiei-we are focusing on finding new intervention targets. RNA interference (RNAi) could be an efficient functional genomics approach to identify such targets. The RNAi pathway is present in S. scabiei and operational in the female adult mite, but other developmental stages have not been assessed. Identifying potential intervention targets in the egg stage is particularly important because current treatments do not kill this latter stage. Here, we established an RNAi tool to silence single-copy genes in S. scabiei eggs. Using sodium hypochlorite pre-treatment, we succeeded in rendering the eggshell permeable to dsRNA without affecting larval hatching. We optimised the treatment of eggs with gene-specific dsRNAs to three single-copy target genes (designated Ss-Cof, Ss-Ddp, and Ss-Nan) which significantly and repeatedly suppressed transcription by ~66.6%, 74.3%, and 84.1%, respectively. Although no phenotypic alterations were detected in dsRNA-treated eggs for Ss-Cof and Ss-Nan, the silencing of Ss-Ddp resulted in a 38% reduction of larval hatching. This RNAi method is expected to provide a useful tool for larger-scale functional genomic investigations for the identification of essential genes as potential drug targets.
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Affiliation(s)
- Deepani D. Fernando
- Infectious Diseases Program, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia;
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3052, Australia; (P.K.K.); (R.B.G.)
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3052, Australia; (P.K.K.); (R.B.G.)
| | - Katja Fischer
- Infectious Diseases Program, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia;
- Correspondence:
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Liu Y, Hu Z, Deng Y, Shang L, Gobler CJ, Tang YZ. Dependence of genome size and copy number of rRNA gene on cell volume in dinoflagellates. Harmful Algae 2021; 109:102108. [PMID: 34815026 DOI: 10.1016/j.hal.2021.102108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Dinoflagellates are an ecologically important group of protists in aquatic environment and have evolved many unusual and enigmatic genomic features such as immense genome sizes, high repeated genes, and a large portion of hydroxymethyluracil in DNA. Although previous studies have observed positive correlations between the large subunit (LSU) rRNA gene copy number and genome size of a variety of eukaryotic organisms (e.g. higher plants and animals), or between cell volume and LSU rRNA gene copy number, and/or between genome size and cell size, which suggests a possible co-evolution among these three features in different lineages of life, it remains an open question regarding the relationships among these three parameters in dinoflagellates. For the first time, we estimated the copy numbers of the LSU rRNA gene, the genome sizes, and cell volumes within a broad range of dinoflagellates (covering 15 species of 11 genera) using single-cell qPCR-based assay (determining LSU rRNA gene copy number), FlowCAM (cell volume measurement), and ultraviolet spectrophotometry (genome size estimation). The measured copy number of LSU rRNA gene ranged from 398 ± 184 (Prorocentrum minimum) to 152,078 ± 33,555 copies•cell-1 (Alexandrium pacificum), while the genome size and the cell volume ranged from 5.6 ± 0.2 (Karlodinium veneficum) to 853 ± 19.9 pg•cell-1 (Pseliodinium pirum), and from 1,070 ± 225 (Kar. veneficum) to 168,474 ± 124,180 μm3 (Ps. pirum), respectively. Together with the three parameters measured in literature, there are significant positive linear correlations between LSU rRNA gene copy numbers and genome sizes, cell volumes and LSU rRNA gene copy numbers, and between genome sizes and cell volumes via comparisons of multi-model regression analyses, suggesting a dependence of genome size and rRNA gene copy number on the cell volumes of dinoflagellates. Validation of the measurement methods was conducted via comparisons between reported data in the literature and that predicted using the linear equations we obtained, and between genome size measured by flow cytometry (FCM) and ultraviolet spectrophotometry (Nanodrop). These results provide insightful understandings of dinoflagellate evolution in terms of the relationships among genomes, gene copy number, and cell volume, and of rRNA gene-based studies in intra-populational and intra-individual genetic diversity, taxonomy, and diversity assessment in the environment of dinoflagellates. The results also provide a dataset useful for reads calibration in environmental metabarcoding studies of dinoflagellates and selection of candidate species for whole genome sequencing.
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Affiliation(s)
- Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lixia Shang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790, USA
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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Kosmala A, Kowalczyk MJ, Żaba R. Dermoscopy, light microscopy, and real-time polymerase chain reaction for the diagnosis of scabies. Preliminary results. Postepy Dermatol Alergol 2021; 38:578-84. [PMID: 34658697 DOI: 10.5114/ada.2020.94275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 12/02/2022] Open
Abstract
Introduction Scabies is a widespread, contagious parasitic disease causing intense itching. Its detection is a significant problem while there are no internationally agreed standards. Aim To compare diagnostic methods: microscopy of skin scrapings, dermoscopy, and real-time polymerase chain reaction (PCR) of skin scrapings and wet skin swabs. Material and methods We included patients with clinical signs of scabies. After dermoscopic evaluation, scrapings were collected from skin lesions and assessed by light microscopy and real-time PCR. Wet skin swabs were also analysed by real-time PCR. Surveys on the presence and severity of pruritus and skin lesions were collected. Seventy-five skin scrapings and 41 wet swabs were examined by real-time PCR. Fifty-three patients completed the survey. All patients underwent dermoscopy and microscopy examinations. 6.67% were positive by microscopy, 10.7% by dermoscopy, 28.0% by real-time PCR from scrapings, and 36.6% when both scrapings and swabs were examined by real-time PCR. All microscopy-positive results were also positive by PCR. Results There was a correlation between real-time PCR from positive scrapings and pruritus (p = 0.023) and body surface area of lesions (p = 0.002), a correlation between copies from wet skin swabs and BSA of lesions (p = 0.002) in the whole group, and a correlation between copies of S. scabiei from scrapings and age (p = 0.038). Conclusions Real-time PCR testing of scrapings and dermoscopy are more effective than microscopy. Combined real-time PCR testing of scrapings and skin swabs seemed the most effective. Clinical signs alone should not be used as unambiguous criteria.
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Korhonen PK, Gasser RB, Ma G, Wang T, Stroehlein AJ, Young ND, Ang CS, Fernando DD, Lu HC, Taylor S, Reynolds SL, Mofiz E, Najaraj SH, Gowda H, Madugundu A, Renuse S, Holt D, Pandey A, Papenfuss AT, Fischer K. High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite. PLoS Negl Trop Dis 2020; 14:e0008720. [PMID: 33001992 PMCID: PMC7591027 DOI: 10.1371/journal.pntd.0008720] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 10/27/2020] [Accepted: 08/17/2020] [Indexed: 12/16/2022] Open
Abstract
The parasitic mite Sarcoptes scabiei is an economically highly significant parasite of the skin of humans and animals worldwide. In humans, this mite causes a neglected tropical disease (NTD), called scabies. This disease results in major morbidity, disability, stigma and poverty globally and is often associated with secondary bacterial infections. Currently, anti-scabies treatments are not sufficiently effective, resistance to them is emerging and no vaccine is available. Here, we report the first high-quality genome and transcriptomic data for S. scabiei. The genome is 56.6 Mb in size, has a a repeat content of 10.6% and codes for 9,174 proteins. We explored key molecules involved in development, reproduction, host-parasite interactions, immunity and disease. The enhanced 'omic data sets for S. scabiei represent comprehensive and critical resources for genetic, functional genomic, metabolomic, phylogenetic, ecological and/or epidemiological investigations, and will underpin the design and development of new treatments, vaccines and/or diagnostic tests.
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Affiliation(s)
- Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Guangxu Ma
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Tao Wang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Andreas J. Stroehlein
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, Victoria, Australia
| | - Deepani D. Fernando
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hieng C. Lu
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sara Taylor
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Simone L. Reynolds
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ehtesham Mofiz
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Shivashankar H. Najaraj
- Faculty of Health, School—Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Harsha Gowda
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Anil Madugundu
- Institute of Bioinformatics, Bangalore, India
- Center for Individualized Medicine and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | | | - Deborah Holt
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- College of Health and Human Sciences, Charles Darwin University, Darwin, Australia
| | - Akhilesh Pandey
- Center for Individualized Medicine and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Anthony T. Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Katja Fischer
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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Mauer K, Hellmann SL, Groth M, Fröbius AC, Zischler H, Hankeln T, Herlyn H. The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala). PLoS One 2020; 15:e0232973. [PMID: 32574180 PMCID: PMC7310846 DOI: 10.1371/journal.pone.0232973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/24/2020] [Indexed: 01/05/2023] Open
Abstract
Thorny-headed worms (Acanthocephala) are endoparasites exploiting Mandibulata (Arthropoda) and Gnathostomata (Vertebrata). Despite their world-wide occurrence and economic relevance as a pest, genome and transcriptome assemblies have not been published before. However, such data might hold clues for a sustainable control of acanthocephalans in animal production. For this reason, we present the first draft of an acanthocephalan nuclear genome, besides the mitochondrial one, using the fish parasite Pomphorhynchus laevis (Palaeacanthocephala) as a model. Additionally, we have assembled and annotated the transcriptome of this species and the proteins encoded. A hybrid assembly of long and short reads resulted in a near-complete P. laevis draft genome of ca. 260 Mb, comprising a large repetitive portion of ca. 63%. Numbers of transcripts and translated proteins (35,683) were within the range of other members of the Rotifera-Acanthocephala clade. Our data additionally demonstrate a significant reorganization of the acanthocephalan gene repertoire. Thus, more than 20% of the usually conserved metazoan genes were lacking in P. laevis. Ontology analysis of the retained genes revealed many connections to the incorporation of carotinoids. These are probably taken up via the surface together with lipids, thus accounting for the orange coloration of P. laevis. Furthermore, we found transcripts and protein sequences to be more derived in P. laevis than in rotifers from Monogononta and Bdelloidea. This was especially the case in genes involved in energy metabolism, which might reflect the acanthocephalan ability to use the scarce oxygen in the host intestine for respiration and simultaneously carry out fermentation. Increased plasticity of the gene repertoire through the integration of foreign DNA into the nuclear genome seems to be another underpinning factor of the evolutionary success of acanthocephalans. In any case, energy-related genes and their proteins may be considered as candidate targets for the acanthocephalan control.
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Affiliation(s)
- Katharina Mauer
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sören Lukas Hellmann
- Molecular Genetics and Genomic Analysis Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Marco Groth
- CF DNA sequencing, Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Andreas C. Fröbius
- Molecular Andrology, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Gießen, Gießen, Germany
| | - Hans Zischler
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Hankeln
- Molecular Genetics and Genomic Analysis Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Holger Herlyn
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
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Bernigaud C, Samarawickrama GR, Jones MK, Gasser RB, Fischer K. The Challenge of Developing a Single-Dose Treatment for Scabies. Trends Parasitol 2019; 35:931-943. [PMID: 31474559 DOI: 10.1016/j.pt.2019.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 11/29/2022]
Abstract
Scabies is a common skin disease with an estimated worldwide incidence of 200 million people infected per year. Its morbidity and mortality is principally due to secondary bacterial infections, a link now well recognized and prompting the recent inclusion of this disease-complex in the WHO list of neglected tropical diseases. The few treatments available are poorly effective against Sarcoptes scabiei eggs and appear to induce resistance in the parasite. An ideal alternative would be a single-dose regimen that kills all developmental stages, including eggs. Drugs used in the veterinary field and applied to other arthropods could be tested experimentally in an established pig-scabies model. Moreover, functional genomics combined with target validation through biochemical research should assist in identifying new drugs.
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Affiliation(s)
- Charlotte Bernigaud
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane 4006, Australia; Dermatology Department, AP-HP, Hôpital Henri Mondor, Université Paris-Est, Créteil, France; Research group Dynamyc, EA7380, Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, Université Paris-Est Créteil, Créteil, France
| | - Gangi R Samarawickrama
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane 4006, Australia
| | - Malcolm K Jones
- School of Veterinary Science, The University of Queensland, Gatton Campus, Gatton, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Australia
| | - Katja Fischer
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane 4006, Australia.
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Dong X, Armstrong SD, Xia D, Makepeace BL, Darby AC, Kadowaki T. Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history. Gigascience 2017; 6:1-17. [PMID: 28327890 PMCID: PMC5467014 DOI: 10.1093/gigascience/gix008] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/01/2017] [Indexed: 01/09/2023] Open
Abstract
The number of managed honey bee colonies has considerably decreased in many developed countries in recent years and ectoparasitic mites are considered as major threats to honey bee colonies and health. However, their general biology remains poorly understood. We sequenced the genome of Tropilaelaps mercedesae, the prevalent ectoparasitic mite infesting honey bees in Asia, and predicted 15 190 protein-coding genes that were well supported by the mite transcriptomes and proteomic data. Although amino acid substitutions have been accelerated within the conserved core genes of two mites, T. mercedesae and Metaseiulus occidentalis, T. mercedesae has undergone the least gene family expansion and contraction between the seven arthropods we tested. The number of sensory system genes has been dramatically reduced, but T. mercedesae contains all gene sets required to detoxify xenobiotics. T. mercedesae is closely associated with a symbiotic bacterium (Rickettsiella grylli-like) and Deformed Wing Virus, the most prevalent honey bee virus. T. mercedesae has a very specialized life history and habitat as the ectoparasitic mite strictly depends on the honey bee inside a stable colony. Thus, comparison of the genome and transcriptome sequences with those of a tick and free-living mites has revealed the specific features of the genome shaped by interaction with the honey bee and colony environment. Genome and transcriptome sequences of T. mercedesae, as well as Varroa destructor (another globally prevalent ectoparasitic mite of honey bee), not only provide insights into the mite biology, but may also help to develop measures to control the most serious pests of the honey bee.
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Affiliation(s)
- Xiaofeng Dong
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou Dushu Lake Higher Education Town, Jiangsu Province 215123, China
| | - Stuart D Armstrong
- Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Dong Xia
- Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Benjamin L Makepeace
- Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou Dushu Lake Higher Education Town, Jiangsu Province 215123, China
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Fernando DD, Marr EJ, Zakrzewski M, Reynolds SL, Burgess STG, Fischer K. Gene silencing by RNA interference in Sarcoptes scabiei: a molecular tool to identify novel therapeutic targets. Parasit Vectors 2017; 10:289. [PMID: 28601087 PMCID: PMC5466799 DOI: 10.1186/s13071-017-2226-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/01/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Scabies is one of the most common and widespread parasitic skin infections globally, affecting a large range of mammals including humans, yet the molecular biology of Sarcoptes scabiei is astonishingly understudied. Research has been hampered primarily due to the difficulty of sampling or culturing these obligatory parasitic mites. A further and major impediment to identify and functionally analyse potential therapeutic targets from the recently emerging molecular databases is the lack of appropriate molecular tools. METHODS We performed standard BLAST based searches of the existing S. scabiei genome databases using sequences of genes described to be involved in RNA interference in Drosophila and the mite model organism Tetranychus urticae. Experimenting with the S. scabiei mu-class glutathione S-transferase (SsGST-mu1) as a candidate gene we explored the feasibility of gene knockdown in S. scabiei by double-stranded RNA-interference (dsRNAi). RESULTS We provide here an analysis of the existing S. scabiei draft genomes, confirming the presence of a double stranded RNA (dsRNA) - mediated silencing machinery. We report for the first time experimental gene silencing by RNA interference (RNAi) in S. scabiei. Non-invasive immersion of S. scabiei in dsRNA encoding an S. scabiei glutathione S-transferase mu-class 1 enzyme (SsGST-mu1) resulted in a 35% reduction in the transcription of the target gene compared to controls. CONCLUSIONS A series of experiments identified the optimal conditions allowing systemic experimental RNAi without detrimental side effects on mite viability. This technique can now be used to address the key questions on the fundamental aspects of mite biology and pathogenesis, and to assess the potential therapeutic benefits of silencing S. scabiei target genes.
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Affiliation(s)
- Deepani D. Fernando
- QIMR Berghofer Medical Research Institute, Infectious Diseases Department, 300 Herston Road, Herston, Brisbane, 4006 Australia
- School of Veterinary Sciences, University of Queensland, Gatton, QLD 4343 Australia
- Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Edward J. Marr
- Parasitology Division, Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, Scotland EH26 0PZ UK
| | - Martha Zakrzewski
- QIMR Berghofer Medical Research Institute, Infectious Diseases Department, 300 Herston Road, Herston, Brisbane, 4006 Australia
| | - Simone L. Reynolds
- QIMR Berghofer Medical Research Institute, Infectious Diseases Department, 300 Herston Road, Herston, Brisbane, 4006 Australia
| | - Stewart T. G. Burgess
- Parasitology Division, Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, Scotland EH26 0PZ UK
| | - Katja Fischer
- QIMR Berghofer Medical Research Institute, Infectious Diseases Department, 300 Herston Road, Herston, Brisbane, 4006 Australia
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13
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Abstract
Background The disease scabies, caused by the ectoparasitic mite, Sarcoptes scabiei, causes significant morbidity in humans and other mammals worldwide. However, there is limited data available regarding the molecular basis of host specificity and host-parasite interactions. Therefore, we sought to produce a draft genome for S. scabiei and use this to identify molecular markers that will be useful for phylogenetic population studies and to identify candidate protein-coding genes that are critical to the unique biology of the parasite. Methods S. scabiei var. canis DNA was isolated from living mites and sequenced to ultra-deep coverage using paired-end technology. Sequence reads were assembled into gapped contigs using de Bruijn graph based algorithms. The assembled genome was examined for repetitive elements and gene annotation was performed using ab initio, and homology-based methods. Results The draft genome assembly was about 56.2 Mb and included a mitochondrial genome contig. The predicted proteome contained 10,644 proteins, ~67 % of which appear to have clear orthologs in other species. The genome also contained more than 140,000 simple sequence repeat loci that may be useful for population-level studies. The mitochondrial genome contained 13 protein coding loci and 20 transfer RNAs. Hundreds of candidate salivary gland protein genes were identified by comparing the scabies mite predicted proteome with sialoproteins and transcripts identified in ticks and other hematophagous arthropods. These include serpins, ferritins, reprolysins, apyrases and new members of the macrophage migration inhibitory factor (MIF) gene family. Numerous other genes coding for salivary proteins, metabolic enzymes, structural proteins, proteins that are potentially immune modulating, and vaccine candidates were identified. The genes encoding cysteine and serine protease paralogs as well as mu-type glutathione S-transferases are represented by gene clusters. S. scabiei possessed homologs for most of the 33 dust mite allergens. Conclusion The draft genome is useful for advancing our understanding of the host-parasite interaction, the biology of the mite and its phylogenetic relationship to other Acari. The identification of antigen-producing genes, candidate immune modulating proteins and pathways, and genes responsible for acaricide resistance offers opportunities for developing new methods for diagnosing, treating and preventing this disease. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-1198-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- S Dean Rider
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA.
| | - Marjorie S Morgan
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA.
| | - Larry G Arlian
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA.
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Abstract
This is the first report of gene silencing by RNA interference (RNAi) in the European house dust mite, Dermatophagoides pteronyssinus, Trouessart, 1897. Using a non-invasive immersion method first developed for the honey bee mite, Varroa destructor, a significant reduction in the expression of D. pteronyssinus glutathione-S-transferase mu-class 1 enzyme (DpGST-mu1) was achieved following overnight immersion in double stranded RNA encoding DpGST-mu1. Although no detrimental phenotypic changes were observed following silencing, this technique can now be used to address fundamental physiological questions and assess the potential therapeutic benefit in silencing D. pteronyssinus target genes in selected domestic situations of high human-mite interface.
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Affiliation(s)
- Edward J Marr
- Division of Vaccines and Diagnostics, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, Scotland, United Kingdom; Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian, Scotland, United Kingdom
| | - Neil D Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian, Scotland, United Kingdom
| | - Alasdair J Nisbet
- Division of Vaccines and Diagnostics, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, Scotland, United Kingdom
| | - Stewart T G Burgess
- Division of Vaccines and Diagnostics, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, Scotland, United Kingdom.
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Husson C, Aguayo J, Revellin C, Frey P, Ioos R, Marçais B. Evidence for homoploid speciation in Phytophthora alni supports taxonomic reclassification in this species complex. Fungal Genet Biol 2015; 77:12-21. [DOI: 10.1016/j.fgb.2015.02.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/18/2015] [Accepted: 02/19/2015] [Indexed: 01/25/2023]
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Marr EJ, Sargison ND, Nisbet AJ, Burgess STG. RNA interference for the identification of ectoparasite vaccine candidates. Parasite Immunol 2015; 36:616-26. [PMID: 25065384 DOI: 10.1111/pim.12132] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/23/2014] [Indexed: 12/21/2022]
Abstract
Ectoparasites present a major challenge for disease management globally. With drug resistance increasingly observed in many disease-causing species, the need for novel control measures is pressing. Ever-expanding genomic resources from 'next generation' sequencing are now available for a number of arthropod ectoparasites, necessitating an effective means of screening these data for novel candidates for vaccine antigens or targets for chemotherapeutics. Such in vitro screening methods must be developed if we are to make discoveries in a timely and cost-effective manner. This review will discuss the potential that RNA interference (RNAi) has demonstrated thus far in the context of arthropod ectoparasites and the potential roles for this technology in the development of novel methods for parasite control.
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Affiliation(s)
- E J Marr
- Division of Vaccines and Diagnostics, Pentlands Science Park, Moredun Research Institute, Bush Loan, Penicuik, Edinburgh, UK; Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian, UK
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Fischer K, Walton S. Parasitic mites of medical and veterinary importance--is there a common research agenda? Int J Parasitol 2014; 44:955-67. [PMID: 25218570 DOI: 10.1016/j.ijpara.2014.08.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 08/22/2014] [Accepted: 08/23/2014] [Indexed: 01/31/2023]
Abstract
There are an estimated 0.5-1 million mite species on earth. Among the many mites that are known to affect humans and animals, only a subset are parasitic but these can cause significant disease. We aim here to provide an overview of the most recent work in this field in order to identify common biological features of these parasites and to inform common strategies for future research. There is a critical need for diagnostic tools to allow for better surveillance and for drugs tailored specifically to the respective parasites. Multi-'omics' approaches represent a logical and timely strategy to identify the appropriate mite molecules. Recent advances in sequencing technology enable us to generate de novo genome sequence data, even from limited DNA resources. Consequently, the field of mite genomics has recently emerged and will now rapidly expand, which is a particular advantage for parasitic mites that cannot be cultured in vitro. Investigations of the microbiota associated with mites will elucidate the link between parasites and pathogens, and define the role of the mite in transmission and pathogenesis. The databases generated will provide the crucial knowledge essential to design novel diagnostic tools, control measures, prophylaxes, drugs and immunotherapies against the mites and associated secondary infections.
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Affiliation(s)
- Katja Fischer
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, Biology Department, Brisbane, Queensland, Australia.
| | - Shelley Walton
- Inflammation and Healing Research Cluster, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.
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Kim JH, Roh JY, Kwon DH, Kim YH, Yoon KA, Yoo S, Noh SJ, Park J, Shin EH, Park MY, Lee SH. Estimation of the genome sizes of the chigger mites Leptotrombidium pallidum and Leptotrombidium scutellare based on quantitative PCR and k-mer analysis. Parasit Vectors 2014; 7:279. [PMID: 24947244 PMCID: PMC4079623 DOI: 10.1186/1756-3305-7-279] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leptotrombidium pallidum and Leptotrombidium scutellare are the major vector mites for Orientia tsutsugamushi, the causative agent of scrub typhus. Before these organisms can be subjected to whole-genome sequencing, it is necessary to estimate their genome sizes to obtain basic information for establishing the strategies that should be used for genome sequencing and assembly. METHOD The genome sizes of L. pallidum and L. scutellare were estimated by a method based on quantitative real-time PCR. In addition, a k-mer analysis of the whole-genome sequences obtained through Illumina sequencing was conducted to verify the mutual compatibility and reliability of the results. RESULTS The genome sizes estimated using qPCR were 191 ± 7 Mb for L. pallidum and 262 ± 13 Mb for L. scutellare. The k-mer analysis-based genome lengths were estimated to be 175 Mb for L. pallidum and 286 Mb for L. scutellare. The estimates from these two independent methods were mutually complementary and within a similar range to those of other Acariform mites. CONCLUSIONS The estimation method based on qPCR appears to be a useful alternative when the standard methods, such as flow cytometry, are impractical. The relatively small estimated genome sizes should facilitate whole-genome analysis, which could contribute to our understanding of Arachnida genome evolution and provide key information for scrub typhus prevention and mite vector competence.
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Affiliation(s)
- Ju Hyeon Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Jong Yul Roh
- Division of Medical Entomology, National Institute of Health, Osong 363-951, Korea
| | - Deok Ho Kwon
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Young Ho Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Kyungjae A Yoon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Seungil Yoo
- Deparment of Research, Codes Division, Insilicogen, Inc, Suwon 441-813, Korea
| | - Seung-Jae Noh
- Deparment of Research, Codes Division, Insilicogen, Inc, Suwon 441-813, Korea
| | - Junhyung Park
- Deparment of Research, Codes Division, Insilicogen, Inc, Suwon 441-813, Korea
| | - E-hyun Shin
- Division of Medical Entomology, National Institute of Health, Osong 363-951, Korea
| | - Mi-Yeoun Park
- Division of Medical Entomology, National Institute of Health, Osong 363-951, Korea
| | - Si Hyeock Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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Abstract
SUMMARY From hundreds of independent transitions from a free-living existence to a parasitic mode of life, separate parasite lineages have converged over evolutionary time to share traits and exploit their hosts in similar ways. Here, we first summarize the evidence that, at a phenotypic level, eukaryotic parasite lineages have all converged toward only six general parasitic strategies: parasitoid, parasitic castrator, directly transmitted parasite, trophically transmitted parasite, vector-transmitted parasite or micropredator. We argue that these strategies represent adaptive peaks, with the similarities among unrelated taxa within any strategy extending to all basic aspects of host exploitation and transmission among hosts and transcending phylogenetic boundaries. Then, we extend our examination of convergent patterns by looking at the evolution of parasite genomes. Despite the limited taxonomic coverage of sequenced parasite genomes currently available, we find some evidence of parallel evolution among unrelated parasite taxa with respect to genome reduction or compaction, and gene losses or gains. Matching such changes in parasite genomes with the broad phenotypic traits that define the convergence of parasites toward only six strategies of host exploitation is not possible at present. Nevertheless, as more parasite genomes become available, we may be able to detect clear trends in the evolution of parasitic genome architectures representing true convergent adaptive peaks, the genomic equivalents of the phenotypic strategies used by all parasites.
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Gregory TR, Nathwani P, Bonnett TR, Huber DPW. Sizing up arthropod genomes: an evaluation of the impact of environmental variation on genome size estimates by flow cytometry and the use of qPCR as a method of estimation. Genome 2013; 56:505-10. [PMID: 24168671 DOI: 10.1139/gen-2013-0044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A study was undertaken to evaluate both a pre-existing method and a newly proposed approach for the estimation of nuclear genome sizes in arthropods. First, concerns regarding the reliability of the well-established method of flow cytometry relating to impacts of rearing conditions on genome size estimates were examined. Contrary to previous reports, a more carefully controlled test found negligible environmental effects on genome size estimates in the fly Drosophila melanogaster. Second, a more recently touted method based on quantitative real-time PCR (qPCR) was examined in terms of ease of use, efficiency, and (most importantly) accuracy using four test species: the flies Drosophila melanogaster and Musca domestica and the beetles Tribolium castaneum and Dendroctonus ponderosa. The results of this analysis demonstrated that qPCR has the tendency to produce substantially different genome size estimates from other established techniques while also being far less efficient than existing methods.
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Affiliation(s)
- T Ryan Gregory
- a Department of Integrative Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
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Mounsey KE, McCarthy JS, Walton SF. Scratching the itch: new tools to advance understanding of scabies. Trends Parasitol 2012; 29:35-42. [PMID: 23088958 DOI: 10.1016/j.pt.2012.09.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/20/2012] [Accepted: 09/21/2012] [Indexed: 12/31/2022]
Abstract
Scabies remains a significant public health problem worldwide. Research into aspects of Sarcoptes scabiei biology and host-parasite interactions has been impeded by an inability to maintain mites in vitro and by limited access to parasite material and infected subjects. The generation of comprehensive expressed sequence tag libraries has enabled the initial characterisation of molecules of interest to diagnostics, vaccines, and drug resistance. The recent development and utilisation of animal models, combined with next-generation technologies, is anticipated to lead to new strategies to prevent, diagnose, and treat scabies, ultimately improving skin health in both human and veterinary settings. This article will summarise recent molecular and immunologic advances on scabies, and will address priorities for the exciting 'next chapter' of scabies research.
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Affiliation(s)
- Kate E Mounsey
- School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, QLD 4558, Australia.
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Holt DC, Burgess STG, Reynolds SL, Mahmood W, Fischer K. Intestinal proteases of free-living and parasitic astigmatid mites. Cell Tissue Res 2012; 351:339-52. [DOI: 10.1007/s00441-012-1369-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 02/08/2012] [Indexed: 11/28/2022]
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Abstract
In 2004, we reviewed the status of disease caused by the scabies mite Sarcoptes scabiei at the time and pointed out that very little basic research had ever been done. The reason for this was largely the lack of availability of mites for experimental purposes and, to a degree, a consequent lack of understanding of its importance, resulting in the trivial name 'itch mite'. Scabies is responsible for major morbidity in disadvantaged communities and immunocompromised patients worldwide. In addition to the physical discomfort caused by the disease, scabies infestations facilitate infection by bacterial pathogens such as Streptococcus pyogenes and Staphylococcus aureus via skin lesions, resulting in severe downstream disease such as in a high prevalence of rheumatic fever/heart disease in affected communities. We now have further evidence that in disadvantaged populations living in tropical climates, scabies rather than 'Strep throat' is an important source of S. pyogenes causing rheumatic fever and eventually rheumatic heart disease. In addition, our work has resulted in two fundamental research tools that facilitate much of the current biomedical research efforts on scabies, namely a public database containing ~45,000 scabies mite expressed sequence tags and a porcine in vivo model. Here we will discuss novel and unexpected proteins encountered in the database that appear crucial to mite survival with regard to digestion and evasion of host defence. The mode(s) of action of some of these have been at least partially revealed. Further, newly discovered molecules that may well have a similar role, such as a family of inactivated cysteine proteases, are yet to be investigated. Hence, there are now whole families of potential targets for chemical inhibitors of S. scabiei. These efforts put today's scabies research in a unique position to design and test small molecules that may specifically interfere with mite-derived molecules, such as digestive proteases and mite complement inhibitors. The porcine scabies model will be available to trial in vivo treatment with potential inhibitors. New therapies for scabies may be developed from these studies and may contribute to reduce the spread of scabies and the subsequent prevalence of bacterial skin infections and their devastating sequelae in the community.
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Affiliation(s)
- Katja Fischer
- Queensland Institute of Medical Research, Herston, Austraria
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