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Bhattacharya S. Episomal and chromosomal DNA replication and recombination in Entamoeba histolytica. Front Mol Biosci 2023; 10:1212082. [PMID: 37363402 PMCID: PMC10285105 DOI: 10.3389/fmolb.2023.1212082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Entamoeba histolytica is the causative agent of amoebiasis. DNA replication studies in E. histolytica first started with the ribosomal RNA genes located on episomal circles. Unlike most plasmids, Entamoeba histolytica rDNA circles lacked a fixed origin. Replication initiated from multiple sites on the episome, and these were preferentially used under different growth conditions. In synchronized cells the early origins mapped within the rDNA transcription unit, while at later times an origin in the promoter-proximal upstream intergenic spacer was activated. This is reminiscent of eukaryotic chromosomal replication where multiple potential origins are used. Biochemical studies on replication and recombination proteins in Entamoeba histolytica picked up momentum once the genome sequence was available. Sequence search revealed homologs of DNA replication and recombination proteins, including meiotic genes. The replicative DNA polymerases identified included the α, δ, ε of polymerase family B; lesion repair polymerases Rev1 and Rev3; a translesion repair polymerase of family A, and five families of polymerases related to family B2. Biochemical analysis of EhDNApolA confirmed its polymerase activity with expected kinetic constants. It could perform strand displacement, and translesion synthesis. The purified EhDNApolB2 had polymerase and exonuclease activities, and could efficiently bypass some types of DNA lesions. The single DNA ligase (EhDNAligI) was similar to eukaryotic DNA ligase I. It was a high-fidelity DNA ligase, likely involved in both replication and repair. Its interaction with EhPCNA was also demonstrated. The recombination-related proteins biochemically characterized were EhRad51 and EhDmc1. Both shared the canonical properties of a recombinase and could catalyse strand exchange over long DNA stretches. Presence of Dmc1 indicates the likelihood of meiosis in this parasite. Direct evidence of recombination in Entamoeba histolytica was provided by use of inverted repeat sequences located on plasmids or chromosomes. In response to a variety of stress conditions, and during encystation in Entamoeba invadens, recombination-related genes were upregulated and homologous recombination was enhanced. These data suggest that homologous recombination could have critical roles in trophozoite growth and stage conversion. Availability of biochemically characterized replication and recombination proteins is an important resource for exploration of novel anti-amoebic drug targets.
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Müller A, Frickmann H, Tannich E, Poppert S, Hagen RM. Colitis caused by Entamoeba histolytica identified by real-time-PCR and fluorescence in situ hybridization from formalin-fixed, paraffin-embedded tissue. Eur J Microbiol Immunol (Bp) 2022; 12:84-91. [PMID: 36136732 PMCID: PMC9530678 DOI: 10.1556/1886.2022.00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/04/2022] [Indexed: 11/19/2022] Open
Abstract
Intestinal amoebiasis in a 35-year-old German patient with a 3 weeks travel history in Indonesia was initially misidentified as non-steroidal anti-inflammatory-drug associated colitis in colonoscopy and histopathological analysis. Furthermore, initial stool examination by microscopy and Entamoeba faecal antigen ELISA did not reveal any protozoan infection. When cessation of non-steroidal anti-inflammatory drug (NSAID) use and mesalazine treatment did not lead to clinical improvement, the patient presented to a specialist for tropical diseases. An intensive reinvestigation including a workup of formalin-fixed, paraffin-embedded colonic biopsies by molecular analysis with real-time PCR and fluorescence in situ hybridization (FISH) proofed the diagnosis of Entamoeba histolytica colitis. Molecular methods including real-time PCR and FISH for the diagnosis of amoebiasis from histopathological samples are rarely used for the diagnosis of E. histolytica infections. Bloody diarrhoea vanished after the onset of metronidazole treatment. In conclusion, the here-presented case demonstrates how modern molecular diagnostics may help to diagnose E. histolytica-associated colitis, even from difficult specimens like paraffin-embedded, formalin-fixed tissue.
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Affiliation(s)
- Andreas Müller
- Department of Tropical Medicine, Missioklinik, 97074Würzburg, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359Hamburg, Germany
- Department of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057Rostock, Germany
| | - Egbert Tannich
- Bernhard Nocht Institute for Tropical Medicine, 20359Hamburg, Germany
| | - Sven Poppert
- Bernhard Nocht Institute for Tropical Medicine, 20359Hamburg, Germany
| | - Ralf Matthias Hagen
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070Koblenz, Germany
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Lagunas-Rangel FA. Ribosomal RNA Transcription Machineries in Intestinal Protozoan Parasites: A Bioinformatic Analysis. Acta Parasitol 2022; 67:1788-1799. [PMID: 36028726 DOI: 10.1007/s11686-022-00612-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE Ribosome biogenesis is a key process in all living organisms, energetically expensive and tightly regulated. Currently, little is known about the components of the ribosomal RNA (rRNA) transcription machinery that are present in intestinal parasites, such as Giardia duodenalis, Cryptosporidium parvum, and Entamoeba histolytica. Thus, in the present work, an analysis was carried out looking for the components of the rRNA transcription machinery that are conserved in intestinal parasites and if these could be used to design new treatment strategies. METHODS The different components of the rRNA transcription machinery were searched in the studied parasites with the NCBI BLAST tool in the EuPathDB Bioinformatics Resource Center database. The sequences of the RRN3 and POLR1F orthologs were aligned and important regions identified. Subsequently, three-dimensional models were built with different bioinformatic tools and a structural analysis was performed. RESULTS Among the protozoa examined, C. parvum is the parasite with the fewest identifiable components of the rRNA transcription machinery. TBP, RRN3, POLR1A, POLR1B, POLR1C, POLR1D, POLR1F, POLR1H, POLR2E, POLR2F and POLR2H subunits were identified in all species studied. Furthermore, the interaction regions between RRN3 and POLR1F were found to be conserved and could be used to design drugs that inhibit rRNA transcription in the parasites studied. CONCLUSION The inhibition of the rRNA transcription machinery in parasites might be a new therapeutic strategy against these microorganisms.
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Transcriptomic analysis of ribosome biogenesis and pre-rRNA processing during growth stress in Entamoeba histolytica. Exp Parasitol 2022; 239:108308. [PMID: 35718007 DOI: 10.1016/j.exppara.2022.108308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 05/27/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022]
Abstract
Ribosome biogenesis, a multi-step process involving transcription, modification, folding and processing of rRNA, is the major consumer of cellular energy. It involves sequential assembly of ribosomal proteins (RP)s via more than 200 ribogenesis factors. Unlike model organisms where transcription of rRNA and RP genes slows down during stress, in Entamoeba histolytica, pre-rRNA synthesis continues, and unprocessed pre-rRNA accumulates. Northern hybridization from different spacer regions depicted the accumulation of unprocessed intermediates during stress. To gain insight into the vast repertoire of ribosome biogenesis factors and understand the major components playing role during stress we computationally identified ribosome biogenesis factors in E. histolytica. Of the ∼279 Saccharomyces cerevisiae proteins, we could only find 188 proteins in E. histolytica. Some of the proteins missing in E. histolytica were also missing in humans. A number of proteins represented by multiple genes in S. cerevisiae had a single copy in E. histolytica. Interestingly E. histolytica lacked mitochondrial ribosome biogenesis factors and had far less RNase components compared to S. cerevisiae. Transcriptomic studies revealed the differential regulation of ribosomal factors both in serum starved and RRP6 down-regulation conditions. These included the NEP1 and TSR3 proteins that chemically modify 18S-rRNA. Pre-rRNA precursors accumulate upon downregulation of the latter proteins in S. cerevisiae and humans. These data reveal the major factors that regulate pre-rRNA processing during stress in E. histolytica and provide the first complete repertoire of ribosome biogenesis factors in this early-branching protist.
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Entamoeba species infection in patients seeking treatment for diarrhea and abdominal discomfort in Mukuru informal settlement in Nairobi, Kenya. Food Waterborne Parasitol 2021; 23:e00122. [PMID: 33898796 PMCID: PMC8053789 DOI: 10.1016/j.fawpar.2021.e00122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/16/2021] [Accepted: 03/21/2021] [Indexed: 01/25/2023] Open
Abstract
Entamoeba histolytica is the only pathogenic species of the Entamoeba genus and is morphologically identical to E. dispar/E. moshkovskii (Entamoeba complex) hence cannot be microscopically differentiated. The other Entamoeba spp. found in humans (E. hartmanni, E. polecki, and E. coli) can be differentiated morphologically from this Entamoeba complex. However, some of their morphologic features overlap making differential diagnosis difficult. This study aimed at determining the occurrence of Entamoeba spp. in patients seeking treatment for diarrhea and/or abdominal discomfort at two clinics in Mukuru informal settlement in Nairobi, Kenya. Faecal samples were collected from 895 patients, examined microscopically following direct wet smear and formal-ether concentration methods. Entamoeba spp. positive faecal samples were subjected to DNA extraction and species-specific nested polymerase chain reaction of the 18S ribosomal RNA (rRNA). By microscopy, Entamoeba spp. cysts or trophozoites were detected in 114/895 (12.7%, 95% Confidence Interval (CI) 10.6-15.1) faecal samples. By nested PCR, the prevalence was: E. histolytica (7.5%, 95% CI 5.9-9.4, 67/895) and E. dispar (8.2%, 95% CI 6.5-10.2, 73/895). Among the Entamoeba spp. complex positive samples, nested PCR detected E. coli and E. hartmanni DNA in 63/114 (55.3%) and 37/114 (32.5%), samples respectively. Among the E. histolytica/E. dispar PCR negative samples (32.5%), 21 (18.4%) contained cysts of either E. coli (19) or E. hartmanni (2) by nested PCR. Entamoeba spp. infections were most common among participants aged 21-30 years; however it was not significant (P = 0.7). Entamoeba spp. infections showed an inverse relationship with diarrhea being most common among participants without diarrhea (P = 0.0). The difference was significant for E. histolytica (P = 0.0) but not significant for E. dispar (P = 0.1). Only E. dispar infections were significantly associated with sex (P = 0.0). This study highlights the need for differentiation of E. histolytica from other Entamoeba spp. by molecular tools for better management of amoebiasis.
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Mon HM, Feng M, Pattanawong U, Kosuwin R, Yanagi T, Kobayashi S, Putaporntip C, Jongwutiwes S, Cheng X, Tachibana H. Genotyping of Entamoeba nuttalli strains from the wild rhesus macaques of Myanmar and comparison with those from the wild rhesus macaques of Nepal and China. INFECTION GENETICS AND EVOLUTION 2021; 92:104830. [PMID: 33798757 DOI: 10.1016/j.meegid.2021.104830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/25/2021] [Accepted: 03/28/2021] [Indexed: 10/21/2022]
Abstract
Entamoeba nuttalli found in macaques is phylogenetically the closest species to Entamoeba histolytica and is potentially pathogenic. In this study, the prevalence of Entamoeba infections was examined in wild rhesus macaques by examining 73 and 90 fecal samples collected from two sites, Popa Taung Kalat (PTK) and Pho Win Taung (PWT), in Myanmar. The positive rates of E. nuttalli detected using PCR were 49% and 31% in PTK and PWT, respectively, but no infections of E. histolytica and E. moshkovskii were found. Entamoeba dispar was detected in 6% of samples only from PWT. Positive rates of E. chattoni and E. coli were both 70% in PWT and 67% and 79% in PTK, respectively. Six E. nuttalli strains from PTK and eight from PWT were obtained in the culture with xenic medium and then, one and two strains, respectively, were axenized and finally cloned. The genotypic analysis of serine-rich protein genes revealed two genotypes each in both sites. The genotypes found in five of six strains from PTK were similar to those from the strains found in Nepal, whereas the remaining one from PTK and two from PWT were similar to those obtained from macaques in China. The sequence of the 18S rDNA of strains with these four genotypes was identical to that of the strains from China. Six loci of tRNA-linked short tandem repeats were analyzed for further genotyping of the strains. Although there were two types in locus A-L in PTK isolates, one of each type for PTK and PWT was found in the other loci, including locus A-L in PWT strains. These results demonstrated that the E. nuttalli strains from Myanmar are closer to the strains from macaques in China rather than those from macaques in Nepal.
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Affiliation(s)
- Hla Myat Mon
- Yangon Technological University, Pharmaceutical Research Department, Myanma Scientific and Technological Research Department, Ministry of Science and Technology, Yangon, Myanmar
| | - Meng Feng
- Department of Parasitology, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan; Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Urassaya Pattanawong
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Rattiporn Kosuwin
- Department of Parasitology, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan; Division of Health Promotion, Faculty of Physical Therapy, Srinakharinwirot University, Ongkharak, Nakhon Nayok 26120, Thailand
| | - Tetsuo Yanagi
- Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Seiki Kobayashi
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Chaturong Putaporntip
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somchai Jongwutiwes
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Xunjia Cheng
- Department of Parasitology, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan; Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Hiroshi Tachibana
- Department of Parasitology, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.
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Mullican JC, Chapman NM, Tracy S. Mapping the Single Origin of Replication in the Naegleria gruberi Extrachromosomal DNA Element. Protist 2019; 170:141-152. [DOI: 10.1016/j.protis.2019.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/28/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
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Saidin S, Othman N, Noordin R. Update on laboratory diagnosis of amoebiasis. Eur J Clin Microbiol Infect Dis 2018; 38:15-38. [DOI: 10.1007/s10096-018-3379-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023]
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Costa JDO, Resende JA, Gil FF, Santos JFG, Gomes MA. Prevalence of Entamoeba histolytica and other enteral parasitic diseases in the metropolitan region of Belo Horizonte, Brazil. A cross-sectional study. SAO PAULO MED J 2018; 136:319-323. [PMID: 30110074 PMCID: PMC9881705 DOI: 10.1590/1516-3180.2018.0036170418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Enteral parasitic diseases are a public health problem in nations with low economic development and in settings with poor sanitation. Amebiasis is the second most frequent form of parasitosis, with a high burden of disease. Knowledge of the prevalence of enteroparasitoses in a given region is useful for planning clinical decision-making. Thus, the aim of this study was to estimate the prevalence of enteral parasitic diseases, especially amebiasis, through analysis on stool samples from public and private laboratories in a metropolitan area in southeastern Brazil. DESIGN AND SETTING Cross-sectional study conducted in the metropolitan region of Belo Horizonte, Brazil. METHODS We evaluated 6,289 fecal samples from one private and one public laboratory. The samples were concentrated by means of spontaneous sedimentation, and those that were positive for Entamoeba histolytica or Entamoeba dispar in optical microscopy analyses were processed to obtain deoxyribonucleic acid, with subsequent identification through the polymerase chain reaction. RESULTS Among the stool samples, 942 (15.0%) had parasitic infections; 73 (1.2%) of these were helminthic infections and 847 (13.5%) were protozoan infections, caused mainly by Escherichia coli (6.0%), Endolimax nana (5.2%) and Giardia lamblia (1.2%). Infections due to Entamoeba histolytica or Entamoeba dispar occurred in 36 samples (0.6%) and the polymerase chain reaction revealed five (13.9%) as Entamoeba histolytica. CONCLUSION The prevalence of enteral parasitic diseases is high in the metropolitan region of Belo Horizonte, although amebiasis may not be a problem.
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Affiliation(s)
- Juliana de Oliveira Costa
- MPH, PharmD. Pharmacist, Department of Social and Preventive Medicine, Postgraduate Program in Public Health, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte (MG), Brazil.
| | - José Adão Resende
- Clinical analysis technician, Hermes Pardini Laboratory, Belo Horizonte (MG), Brazil.
| | - Frederico Ferreira Gil
- PhD. Nurse, Department of Parasitology, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte (MG), Brazil.
| | | | - Maria Aparecida Gomes
- PharmD, PhD. Full Professor, Department of Parasitology, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte (MG), Brazil.
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Vlčková K, Kreisinger J, Pafčo B, Čížková D, Tagg N, Hehl AB, Modrý D. Diversity of Entamoeba spp. in African great apes and humans: an insight from Illumina MiSeq high-throughput sequencing. Int J Parasitol 2018. [PMID: 29530647 DOI: 10.1016/j.ijpara.2017.11.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the complex Entamoeba communities in the mammalian intestine has been, to date, complicated by the lack of a suitable approach for molecular detection of multiple variants co-occurring in mixed infections. Here, we report on the application of a high throughput sequencing approach based on partial 18S rDNA using the Illumina MiSeq platform. We describe, to our knowledge, for the first time, the Entamoeba communities in humans, free-ranging western lowland gorillas and central chimpanzees living in the Dja Faunal Reserve in Cameroon. We detected 36 Entamoeba haplotypes belonging to six haplotype clusters, containing haplotypes possessing high and low host specificity. Most of the detected haplotypes belonged to commensal Entamoeba, however, the pathogenic species (Entamoeba histolytica and Entamoeba nuttalli) were also detected. We observed that some Entamoeba haplotypes are shared between humans and other hosts, indicating their zoonotic potential. The findings are important not only for understanding the epidemiology of amoebiasis in humans in rural African localities, but also in the context of wild great ape conservation.
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Affiliation(s)
- Klára Vlčková
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, Brno 61242, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, Brno 603 65, Czech Republic.
| | - Jakub Kreisinger
- Division of Animal Evolutionary Biology, Department of Zoology Faculty of Science, Charles University in Prague, Viničná 7, 128 44 Praha, Czech Republic
| | - Barbora Pafčo
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, Brno 61242, Czech Republic
| | - Dagmar Čížková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, Brno 603 65, Czech Republic
| | - Nikki Tagg
- Projet Grands Singes Cameroon, Centre for Research and Conservation, Royal Zoological Society of Antwerp, 20-26 Koningin Astridplein, 2018 Antwerp, Belgium
| | - Adrian B Hehl
- Institute of Parasitology, University of Zurich, Winterthurerstrasse 266a, CH-8057 Zrich, Switzerland
| | - David Modrý
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, Brno 61242, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 370 05, Czech Republic; CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, Brno 612 42, Czech Republic
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Molecular Diagnosis of Gastrointestinal Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Forsell J, Koskiniemi S, Hedberg I, Edebro H, Evengård B, Granlund M. Evaluation of factors affecting real-time PCR performance for diagnosis of Entamoeba histolytica and Entamoeba dispar in clinical stool samples. J Med Microbiol 2015; 64:1053-1062. [PMID: 26296348 DOI: 10.1099/jmm.0.000129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although PCR offers the potential for sensitive detection of parasites there are several pitfalls for optimal performance, especially when DNA is extracted from a complex sample material such as stool. With the aid of a sensitive inhibitor control in a duplex real-time PCR (qPCR) for identification of Entamoeba histolytica and Entamoeba dispar we have evaluated factors that influenced the performance of the qPCR and have suggested a rationale to be used in the analysis of clinical samples. Pre-PCR processing was found to be of outmost importance for an optimal amplification since inhibitors caused false-negative results when higher amounts of sample were used. Stool sampling with a flocked swab (ESwab, Copan), yielding on average 173 mg, gave positive qPCR results in samples with cysts of E. dispar that were negative in serially diluted stool samples. The degree of inhibition found varied between samples and was not an on-off phenomenon. Even low-grade inhibition, shown as an increase of two cycles in the qPCR for the inhibitor control, could lead to false negativity in samples with low amounts of parasites. Lack of amplification in the qPCR due to inhibition could be overcome by dilution of the extracted DNA by 1/10-1/20. We also describe the use of guanidinium thiocyanate buffer for transport and storage of samples as well as a time-saving semi-automated DNA extraction method in an Arrow instrument (Nordiag) preceded by bead beating.
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Affiliation(s)
- Joakim Forsell
- Division of Clinical Bacteriology, Department of Clinical Microbiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Satu Koskiniemi
- Division of Clinical Bacteriology, Department of Clinical Microbiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Ida Hedberg
- Division of Clinical Bacteriology, Department of Clinical Microbiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Helén Edebro
- Division of Clinical Bacteriology, Department of Clinical Microbiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Birgitta Evengård
- Division of Infectious diseases, Department of Clinical Microbiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Margareta Granlund
- Division of Clinical Bacteriology, Department of Clinical Microbiology, Umeå University, SE-901 87 Umeå, Sweden
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Das K, Ganguly S. Evolutionary genomics and population structure of Entamoeba histolytica. Comput Struct Biotechnol J 2014; 12:26-33. [PMID: 25505504 PMCID: PMC4262060 DOI: 10.1016/j.csbj.2014.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 01/02/2023] Open
Abstract
Amoebiasis caused by the gastrointestinal parasite Entamoeba histolytica has diverse disease outcomes. Study of genome and evolution of this fascinating parasite will help us to understand the basis of its virulence and explain why, when and how it causes diseases. In this review, we have summarized current knowledge regarding evolutionary genomics of E. histolytica and discussed their association with parasite phenotypes and its differential pathogenic behavior. How genetic diversity reveals parasite population structure has also been discussed. Queries concerning their evolution and population structure which were required to be addressed have also been highlighted. This significantly large amount of genomic data will improve our knowledge about this pathogenic species of Entamoeba.
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Affiliation(s)
- Koushik Das
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, Kolkata 700010, India
| | - Sandipan Ganguly
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, Kolkata 700010, India
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Influence of parasite density and sample storage time on the reliability of Entamoeba histolytica-specific PCR from formalin-fixed and paraffin-embedded tissues. ACTA ACUST UNITED AC 2014; 22:236-44. [PMID: 24193008 DOI: 10.1097/pdm.0b013e3182936936] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report on the reliability of polymerase chain reaction (PCR) for the detection of Entamoeba histolytica from formalin-fixed, paraffin-embedded tissue in comparison with microscopy and have determined predictors that may influence PCR results. E. histolytica-specific and Entamoeba dispar-specific real-time PCR and microscopy from adjacent histologic sections were performed using a collection of formalin-fixed, paraffin-embedded tissue specimens obtained from patients with invasive amebiasis. Specimens had been collected during the previous 4 decades. Association of sample age, parasite density, and reliability of PCR was analyzed. E. histolytica PCR was positive in 20 of 34 biopsies (58.8%); 2 of these 20 were microscopically negative for amebae in neighboring tissue sections. PCR was negative in 9 samples with visible amebae in neighboring sections and in 5 samples without visible parasites in neighboring sections. PCR was negative in all specimens that were older than 3 decades. Low parasite counts and sample ages older than 20 years were predictors for false-negative PCR results. All samples were negative for E. dispar DNA. PCR is suitable for the detection of E. histolytica in formalin-fixed, paraffin-embedded tissue samples that are younger than 2 decades and that contain intermediate to high parasite numbers. Negative results in older samples were due to progressive degradation of DNA over time as indicated by control PCRs targeting the human 18S rRNA gene. Moreover, our findings support previous suggestions that only E. histolytica but not E. dispar is responsible for invasive amebiasis.
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Srivastava A, Ahamad J, Ray AK, Kaur D, Bhattacharya A, Bhattacharya S. Analysis of U3 snoRNA and small subunit processome components in the parasitic protist Entamoeba histolytica. Mol Biochem Parasitol 2014; 193:82-92. [PMID: 24631428 DOI: 10.1016/j.molbiopara.2014.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 10/25/2022]
Abstract
In the early branching parasitic protist Entamoeba histolytica, pre-rRNA synthesis continues when cells are subjected to growth stress, but processing slows down and unprocessed pre-rRNA accumulates. To gain insight into the regulatory mechanisms leading to accumulation, it is necessary to define the pre-rRNA processing machinery in E. histolytica. We searched the E. histolytica genome sequence for homologs of the SSU processome, which contains the U3snoRNA, and 72 proteins in yeast. We could identify 57 of the proteins with high confidence. Of the rest, 6 were absent in human, and 4 were non-essential in yeast. The remaining 5 were absent in other parasite genomes as well. Analysis of U3snoRNA showed that the E. histolytica U3snoRNA adopted the same conserved secondary structure as seen in yeast and human. The predicted structure was verified by chemical modification followed by primer extension (SHAPE). Further we showed that the predicted interactions of Eh_U3snoRNA boxes A and A' with pre-18S rRNA were highly conserved both in position and sequence. The predicted interactions of 5'-hinge and 3'-hinge sequences of Eh_U3 snoRNA with the 5'-ETS sequences were conserved in position but not in sequence. Transcription of selected genes of SSU processome was tested by northern analysis, and transcripts of predicted sizes were obtained. During serum starvation, when unprocessed pre-RNA accumulated, the transcript levels of some of these genes declined. This is the first report on pre-rRNA processing machinery in E. histolytica, and shows that the components are well conserved with respect to yeast and human.
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Affiliation(s)
- Ankita Srivastava
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Jamaluddin Ahamad
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Ashwini Kumar Ray
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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Zhang H, Ehrenkaufer GM, Hall N, Singh U. Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes. BMC Genomics 2013; 14:53. [PMID: 23347563 PMCID: PMC3610107 DOI: 10.1186/1471-2164-14-53] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 01/02/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Small RNA mediated gene silencing is a well-conserved regulatory pathway. In the parasite Entamoeba histolytica an endogenous RNAi pathway exists, however, the depth and diversity of the small RNA population remains unknown. RESULTS To characterize the small RNA population that associates with E. histolytica Argonaute-2 (EhAGO2-2), we immunoprecipitated small RNAs that associate with it and performed one full pyrosequencing run. Data analysis revealed new features of the 27nt small RNAs including the 5'-G predominance, distinct small RNA distribution patterns on protein coding genes, small RNAs mapping to both introns and exon-exon junctions, and small RNA targeted genes that are clustered particularly in sections of genome duplication. Characterization of genomic loci to which both sense and antisense small RNAs mapped showed that both sets of small RNAs have 5'-polyphosphate termini; strand-specific RT-PCR detected transcripts in both directions at these loci suggesting that both transcripts may serve as template for small RNA generation. In order to determine whether small RNA abundance patterns account for strain-specific gene expression profiles of E. histolytica virulent and non-virulent strains, we sequenced small RNAs from a non-virulent strain and found that small RNAs mapped to genes in a manner consistent with their regulation of strain-specific virulence genes. CONCLUSIONS We provided a full spectrum analysis for E. histolytica AGO2-2 associated 27nt small RNAs. Additionally, comparative analysis of small RNA populations from virulent and non-virulent amebic strains indicates that small RNA populations may regulate virulence genes.
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Affiliation(s)
- Hanbang Zhang
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305-5107, USA
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17
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Glöckner G, Noegel AA. Comparative genomics in the Amoebozoa clade. Biol Rev Camb Philos Soc 2012; 88:215-25. [PMID: 23134060 DOI: 10.1111/j.1469-185x.2012.00248.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 09/25/2012] [Accepted: 10/05/2012] [Indexed: 11/30/2022]
Abstract
Amoeboid life forms can be found throughout the evolutionary tree. The greatest proportion of these life forms is found in the Amoebozoa clade, one of the six major eukaryote evolutionary branches. Despite its common origin this clade exhibits a wide diversity of lifestyles including free-living and parasitic species and species with multicellular and multinucleate life stages. In this group, development, cooperation, and social behaviour can be studied in addition to traits common to unicellular organisms. To date, only a few Amoebozoa genomes have been sequenced completely, however a number of expressed sequence tags (ESTs) and complete and draft genomes have become available recently for several species that represent some of the major evolutionary lineages in this clade. This resource allows us to compare and analyse the evolutionary history and fate of branch-specific genes if properly exploited. Despite the large evolutionary time scale since the emergence of the major groups the genomic organization in Amoebozoa has retained common features. The number of Amoebozoa-specific genetic inventions seems to be rather small. The emergence of subgroups is accompanied by gene and domain losses and acquisitions of bacterial gene material. The sophisticated developmental cycles of Myxogastria and Dictyosteliida likely have a common origin and are deeply rooted in amoebozoan evolution. In this review we describe initial approaches to comparative genomics in Amoebozoa, summarize recent findings, and identify goals for further studies.
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Affiliation(s)
- Gernot Glöckner
- Institute for Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301, Berlin, D-12587, Germany.
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18
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Abstract
Genomic analyses increasingly make use of sophisticated statistical and computational approaches in investigations of genomic function and evolution. Scientists implementing and developing these approaches are often computational scientists, physicists, or mathematicians. This article aims to provide a compact overview of genome biology for these scientists. Thus, the article focuses on providing biological context to the genomic features, processes, and structures analysed by these approaches. Topics covered include (1) differences between eukaryotic and prokaryotic cells; (2) the physical structure of genomes and chromatin; (3) different categories of genomic regions, including those serving as templates for RNA and protein synthesis, regulatory regions, repetitive regions, and "architectural" or "organisational" regions, such as centromeres and telomeres; (4) the cell cycle; (5) an overview of transcription, translation, and protein structure; and (6) a glossary of relevant terms.
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19
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Gupta AK, Panigrahi SK, Bhattacharya A, Bhattacharya S. Self-circularizing 5'-ETS RNAs accumulate along with unprocessed pre ribosomal RNAs in growth-stressed Entamoeba histolytica. Sci Rep 2012; 2:303. [PMID: 22396851 PMCID: PMC3294279 DOI: 10.1038/srep00303] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 02/15/2012] [Indexed: 01/13/2023] Open
Abstract
The primary transcript of rRNA genes is a large pre rRNA which is precisely processed to release the mature rRNAs. The 5'-external transcribed spacer (ETS) of rRNA genes contains important sites for pre rRNA processing. Once the processing is accomplished the ETS is rapidly degraded. We show that in growth-stressed cells of the human parasitic protist Entamoeba histolytica the A'-A(0) sub-fragment of the 5'-ETS accumulates to high levels as a family of RNA molecules of size 666 to 912 nt. These etsRNAs are circular in vivo and can spontaneously self-circularize in vitro. The accumulation of etsRNAs is accompanied by accumulation of unprocessed pre rRNA, indicating a possible role of etsRNAs in inhibition of processing during growth stress. Our data shows for the first time that processed etsRNA is not a mere by-product destined for degradation but is stabilized by circularization and could play a regulatory role as noncoding RNA.
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20
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Molecular Diagnosis of Gastrointestinal Infections. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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The Naegleria genome: a free-living microbial eukaryote lends unique insights into core eukaryotic cell biology. Res Microbiol 2011; 162:607-18. [PMID: 21392573 DOI: 10.1016/j.resmic.2011.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/29/2011] [Indexed: 11/24/2022]
Abstract
Naegleria gruberi, a free-living protist, has long been treasured as a model for basal body and flagellar assembly due to its ability to differentiate from crawling amoebae into swimming flagellates. The full genome sequence of Naegleria gruberi has recently been used to estimate gene families ancestral to all eukaryotes and to identify novel aspects of Naegleria biology, including likely facultative anaerobic metabolism, extensive signaling cascades, and evidence for sexuality. Distinctive features of the Naegleria genome and nuclear biology provide unique perspectives for comparative cell biology, including cell division, RNA processing and nucleolar assembly. We highlight here exciting new and novel aspects of Naegleria biology identified through genomic analysis.
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22
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Boesler C, Kruse J, Söderbom F, Hammann C. Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum. J Biol Chem 2011; 286:17693-703. [PMID: 21454536 DOI: 10.1074/jbc.m110.208306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The amoeba Dictyostelium discoideum is a well established model organism for studying numerous aspects of cellular and developmental functions. Its ribosomal RNA (rRNA) is encoded in an extrachromosomal palindrome that exists in ∼100 copies in the cell. In this study, we have set out to investigate the sequence of the expressed rRNA. For this, we have ligated the rRNA ends and performed RT-PCR on these circular RNAs. Sequencing revealed that the mature 26 S, 17 S, 5.8 S, and 5 S rRNAs have sizes of 3741, 1871, 162, and 112 nucleotides, respectively. Unlike the published data, all mature rRNAs of the same type uniformly display the same start and end nucleotides in the analyzed AX2 strain. We show the existence of a short lived primary transcript covering the rRNA transcription unit of 17 S, 5.8 S, and 26 S rRNA. Northern blots and RT-PCR reveal that from this primary transcript two precursor molecules of the 17 S and two precursors of the 26 S rRNA are generated. We have also determined the sequences of these precursor molecules, and based on these data, we propose a model for the maturation of the rRNAs in Dictyostelium discoideum that we compare with the processing of the rRNA transcription unit of Saccharomyces cerevisiae.
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Affiliation(s)
- Carsten Boesler
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, 64287 Darmstadt, Germany
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23
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Weedall GD, Hall N. Evolutionary genomics of Entamoeba. Res Microbiol 2011; 162:637-45. [PMID: 21288488 PMCID: PMC3268252 DOI: 10.1016/j.resmic.2011.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 12/17/2010] [Indexed: 11/06/2022]
Abstract
Entamoeba histolytica is a human pathogen that causes amoebic dysentery and leads to significant morbidity and mortality worldwide. Understanding the genome and evolution of the parasite will help explain how, when and why it causes disease. Here we review current knowledge about the evolutionary genomics of Entamoeba: how differences between the genomes of different species may help explain different phenotypes, and how variation among E. histolytica parasites reveals patterns of population structure. The imminent expansion of the amount genome data will greatly improve our knowledge of the genus and of pathogenic species within it.
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Affiliation(s)
- Gareth D Weedall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
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24
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Kong HH. Molecular phylogeny of acanthamoeba. THE KOREAN JOURNAL OF PARASITOLOGY 2010; 47 Suppl:S21-8. [PMID: 19885332 DOI: 10.3347/kjp.2009.47.s.s21] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 10/05/2009] [Accepted: 10/05/2009] [Indexed: 11/23/2022]
Abstract
After morphological grouping of Acanthamoeba by Pussard and Pons, phylogeny of the genus has been always a big topic to the researchers. Because of the variability of morphological characteristics, unchangeable and stable characters have been investigated for phylogenic criteria. Isoenzyme and mitochondrial DNA RFLP (Mt DNA RFLP) analyses revealed different patterns among strains assigned to a same species. Therefore, these characteristics would be considered as tools for strain discrimination than species identification. The most recently developed and the most promising method is the sequence analysis of 18s ribosomal RNA coding DNA (18s rDNA). The phylogenic tree based on comparison of 18s rDNA sequences distinguished the 3 morphological groups of Acanthamoeba and divided them into 12 unique sequence types (T1-T12 genotypes). Most clinical and environmental isolates belonged to the morphological group II and the genotype T4. In the Republic of Korea, 2 strains of Acanthamoeba, YM-2 and YM-3, were first isolated from the environment in 1974. However, phylogenic identification of Korean Acanthamoeba isolates from human infections or the environment were tried from the late 1990s. By RFLP analysis or total sequence analysis of 18s rDNA revealed that almost all clinical isolates including the one from a suspicious granulomatous amebic encephalitis patient belonged to the genotype T4. A large number of environmental isolates from contact lens storage cases, tapped water, and ocean sediments also belonged to the genotype T4. Almost identical strain characteristics, such as Mt DNA RFLP pattern of environmental isolates, with the clinical isolates could make a simple conclusion that most environmental isolates might be a potential keratopathogen.
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Affiliation(s)
- Hyun Hee Kong
- Department of Parasitology, Kyungpook National University School of Medicine, Daegu 700-422, Korea.
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25
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Torres-Machorro AL, Hernández R, Cevallos AM, López-Villaseñor I. Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny? FEMS Microbiol Rev 2010; 34:59-86. [DOI: 10.1111/j.1574-6976.2009.00196.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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An alternative method for DNA extraction and PCR identification of Entamoeba histolytica and E. dispar in fecal samples. Parasitology 2009; 136:765-9. [PMID: 19486545 DOI: 10.1017/s0031182009006167] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Since it is known that Entamoeba dispar is non-pathogenic and morphologically similar to E. histolytica, there are many targets used in PCR for differentiating these species. However, obtaining high quality DNA from fecal samples is fundamental for PCR. Most methods are laborious or use kits that make diagnosis expensive. In the present work, a new simple, fast and cheap technique of DNA extraction from fecal samples was combined with a PCR for an episomal target in order to identify E. histolytica and E. dispar in feces.
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27
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Jhingan GD, Panigrahi SK, Bhattacharya A, Bhattacharya S. The nucleolus in Entamoeba histolytica and Entamoeba invadens is located at the nuclear periphery. Mol Biochem Parasitol 2009; 167:72-80. [PMID: 19416742 DOI: 10.1016/j.molbiopara.2009.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 04/21/2009] [Accepted: 04/24/2009] [Indexed: 10/20/2022]
Abstract
The ribosomal RNA genes in the human parasite Entamoeba histolytica and its reptilian counterpart Entamoeba invadens are located on extrachromosomal circles. The expression of rRNA genes generally takes place in a specialized nuclear compartment-the nucleolus. In Entamoeba species the nuclear space that may be called the nucleolus has yet to be defined. Previous studies showed that the rDNA circles are located at the nuclear periphery. Here we have raised antibodies against the E. histolytica homologue of fibrillarin, a highly conserved protein known to be a marker for nucleolus. These antibodies cross-reacted preferentially with the nuclear periphery, forming a peripheral ring. There was complete colocalization of fibrillarin with the signal obtained by antibodies against E. histolytica RNA polymerase I (but not polymerase II and III), strongly suggesting that the nucleolus in E. histolytica is indeed located at the nuclear periphery. The dynamic nature of the nucleolus was evident when cells were subjected to a variety of growth stresses. Although the peripheral nucleolar structure was retained, stress was accompanied by significant cytoplasmic localization of RNA polymerase I, and to some extent fibrillarin. The nucleolus in E. invadens was also located at the nuclear periphery. When these cells were induced to encyst the nucleolar ring structure was lost, giving way to small, fragmented foci. This study gives the first clear insight into nucleolar structure in Entamoeba.
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Affiliation(s)
- Gagan Deep Jhingan
- School of Environmental Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
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28
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Solaymani-Mohammadi S, Coyle CM, Factor SM, Petri WA. Amebic colitis in an antigenically and serologically negative patient: usefulness of a small-subunit ribosomal RNA gene-based polymerase chain reaction in diagnosis. Diagn Microbiol Infect Dis 2008; 62:333-5. [PMID: 18691843 PMCID: PMC2601554 DOI: 10.1016/j.diagmicrobio.2008.06.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Revised: 06/12/2008] [Accepted: 06/25/2008] [Indexed: 10/21/2022]
Abstract
Specific identification of Entamoeba histolytica in clinical specimens is an essential confirmatory diagnostic step in the management of amebiasis. Here, we report an unusual case of amebic colitis in a 20-year-old female immigrant from South China. The patient had experienced diarrhea, crampy abdominal pain, and fever for approximately 3 weeks prior to admission to hospital and had treated herself at home with metronidazole. On admission, stool microscopy and serology for E. histolytica were negative. Because the clinical findings raised the suspicion of Clostridium difficile fulminant colitis, she underwent a subtotal colectomy. Histopathology revealed flask-shaped ulcers characteristic of amebic colitis. Consequently, E. histolytica DNA was detected by a sensitive small-subunit rRNA polymerase chain reaction (PCR) from feces, and the patient was successfully treated for amebiasis with metronidazole. This case exemplifies the relative insensitivity of serologic tests for the diagnosis of intestinal amebiasis and the difficulties encountered in detecting the parasite antigen in a patient partially treated with metronidazole. We conclude that when the possibility of invasive intestinal amebiasis is suspected, detecting the parasite DNA directly in the stool sample by PCR using E. histolytica-specific primers may be an alternative, noninvasive, and reliable tool for the specific diagnosis of the disease.
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Affiliation(s)
- Shahram Solaymani-Mohammadi
- Division of Intestinal and Genital Protozoal Diseases, Department of Medical Parasitology and Mycology, School of Public Health and Institute of Public Health Research, Tehran University of Medical Sciences, PO Box 14155, Tehran 6446, Iran
- Division of Infectious Diseases and International Health, University of Virginia Health System, MR4 Building, Room 2115, Lane Road, P.O. Box 801340, Charlottesville, VA 22908-1340, USA
| | - Christina M. Coyle
- Division of Infectious Diseases, Department of Medicine, Room 3N21, Jacobi Medical Center, Albert Einstein College of Medicine, 1400 Pelham Parkway South, Bronx, New York 10461, USA
| | - Stephen M. Factor
- Division of Tropical Medicine and Parasitology, Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - William A. Petri
- Division of Infectious Diseases and International Health, University of Virginia Health System, MR4 Building, Room 2115, Lane Road, P.O. Box 801340, Charlottesville, VA 22908-1340, USA
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29
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Promoter analysis of palindromic transcription units in the ribosomal DNA circle of Entamoeba histolytica. EUKARYOTIC CELL 2008; 8:69-76. [PMID: 18978203 DOI: 10.1128/ec.00254-08] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
rRNA genes of Entamoeba histolytica are organized as palindromic ribosomal DNA (rDNA) units (I and II) in a 24.5-kb circle. Although the two rDNAs are identical in sequence, their upstream spacers are completely different. Since the intergenic sequences (IGS) of all rDNA copies in other organisms are conserved and contain transcription regulatory sequences, the lack of sequence conservation in the IGS prompted the question of whether both rDNAs are indeed transcriptionally active. We mapped the transcriptional start points (tsp's) and promoters of the two rDNAs. A 51-bp sequence immediately upstream of the tsp's was highly conserved in both units. In addition, both units had an A+T-rich stretch upstream of the 51-bp core. Analysis of reporter gene transcription showed promoter activity to reside in the regions from positions -86 to +123 (rDNA I) and positions -101 to +140 (rDNA II). The promoter-containing fragments from both units could bind and compete with each other for protein(s) from nuclear extracts. Protein binding was especially dependent on the A+T-rich region upstream of the 51-bp core (positions -53 to -68). The requirement of >80 bp downstream of the tsp was striking. Although this sequence was not conserved in the two units, it could potentially fold into very long stem-loops. Both rDNAs transcribed with comparable efficiency, as measured by nuclear runon. Thus, both rDNAs share very similar organization of promoter sequences, and in exponential culture both rDNAs are transcribed. It remains to be seen whether the different IGS affect the regulation of the two units under adverse conditions.
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30
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Mukherjee C, Clark CG, Lohia A. Entamoeba shows reversible variation in ploidy under different growth conditions and between life cycle phases. PLoS Negl Trop Dis 2008; 2:e281. [PMID: 18714361 PMCID: PMC2500184 DOI: 10.1371/journal.pntd.0000281] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Accepted: 07/18/2008] [Indexed: 11/18/2022] Open
Abstract
Under axenic growth conditions, trophozoites of Entamoeba histolytica contain heterogenous amounts of DNA due to the presence of both multiple nuclei and different amounts of DNA in individual nuclei. In order to establish if the DNA content and the observed heterogeneity is maintained during different growth conditions, we have compared E. histolytica cells growing in xenic and axenic cultures. Our results show that the nuclear DNA content of E. histolytica trophozoites growing in axenic cultures is at least 10 fold higher than in xenic cultures. Re-association of axenic cultures with their bacterial flora led to a reduction of DNA content to the original xenic values. Thus switching between xenic and axenic growth conditions was accompanied by significant changes in the nuclear DNA content of this parasite. Changes in DNA content during encystation-excystation were studied in the related reptilian parasite E. invadens. During excystation of E. invadens cysts, it was observed that the nuclear DNA content increased approximately 40 fold following emergence of trophozoites in axenic cultures. Based on the observed large changes in nuclear size and DNA content, and the minor differences in relative abundance of representative protein coding sequences, rDNA and tRNA sequences, it appears that gain or loss of whole genome copies may be occurring during changes in the growth conditions. Our studies demonstrate the inherent plasticity and dynamic nature of the Entamoeba genome in at least two species. In contrast to the perception that DNA content of an organism is stable and maintained during different conditions and life cycle stages, new evidence shows that many organisms display changes in their DNA content at different stages of their life cycle. We have earlier identified intra-cellular and inter-cellular differences in DNA content of the protist pathogen Entamoeba histolytica and established that this organism can tolerate large variations in DNA content during axenic culture. In this study we have made an important advancement in the understanding of amoeba biology where we have shown that changes in growth conditions and life cycle stages are accompanied by large differences in DNA content involving gain or loss of whole genome copies. This property may well regulate the outcome of infection and subsequently the disease.
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Affiliation(s)
| | - C. Graham Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Anuradha Lohia
- Department of Biochemistry, Bose Institute, Kolkata, India
- * E-mail:
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31
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Abstract
The genomic peculiarities among microbial eukaryotes challenge the conventional wisdom of genome evolution. Currently, many studies and textbooks explore principles of genome evolution from a limited number of eukaryotic lineages, focusing often on only a few representative species of plants, animals and fungi. Increasing emphasis on studies of genomes in microbial eukaryotes has and will continue to uncover features that are either not present in the representative species (e.g. hypervariable karyotypes or highly fragmented mitochondrial genomes) or are exaggerated in microbial groups (e.g. chromosomal processing between germline and somatic nuclei). Data for microbial eukaryotes have emerged from recent genome sequencing projects, enabling comparisons of the genomes from diverse lineages across the eukaryotic phylogenetic tree. Some of these features, including amplified rDNAs, subtelomeric rDNAs and reduced genomes, appear to have evolved multiple times within eukaryotes, whereas other features, such as absolute strand polarity, are found only within single lineages.
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Affiliation(s)
- Casey L McGrath
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
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32
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Clark CG, Alsmark UCM, Tazreiter M, Saito-Nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noël CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillén N, Duchêne M, Nozaki T, Hall N. Structure and content of the Entamoeba histolytica genome. ADVANCES IN PARASITOLOGY 2008; 65:51-190. [PMID: 18063096 DOI: 10.1016/s0065-308x(07)65002-7] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The intestinal parasite Entamoeba histolytica is one of the first protists for which a draft genome sequence has been published. Although the genome is still incomplete, it is unlikely that many genes are missing from the list of those already identified. In this chapter we summarise the features of the genome as they are currently understood and provide previously unpublished analyses of many of the genes.
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Affiliation(s)
- C G Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Zufall RA, Robinson T, Katz LA. Evolution of developmentally regulated genome rearrangements in eukaryotes. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2005; 304:448-55. [PMID: 16032699 DOI: 10.1002/jez.b.21056] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Developmentally regulated genome rearrangements (DRGR)--processes that alter genomes either in specific cells or during specific life cycle stages--are widespread throughout eukaryotes. This contrasts with the view that genome structure and content remain essentially constant throughout an organism's life cycle. Here we review three categories of developmentally regulated genome processing in eukaryotes: genome-wide rearrangements, targeted rearrangements, and a special case of amplification of ribosomal DNA genes. Mapping these types of DRGR onto eukaryotic phylogeny indicates that each type of processing is found in multiple independent lineages. We propose that such genome rearrangements were present within the last common ancestor of extant eukaryotes, and that future research will yield evidence of homologous epigenetic mechanisms underlying genome processing among diverse eukaryotes.
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Affiliation(s)
- Rebecca A Zufall
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA.
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35
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Qvarnstrom Y, James C, Xayavong M, Holloway BP, Visvesvara GS, Sriram R, da Silva AJ. Comparison of real-time PCR protocols for differential laboratory diagnosis of amebiasis. J Clin Microbiol 2005; 43:5491-7. [PMID: 16272475 PMCID: PMC1287814 DOI: 10.1128/jcm.43.11.5491-5497.2005] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Revised: 07/08/2005] [Accepted: 08/15/2005] [Indexed: 11/20/2022] Open
Abstract
Specific identification of Entamoeba spp. in clinical specimens is an important confirmatory diagnostic step in the management of patients who may be infected with Entamoeba histolytica, the species that causes clinical amebiasis. Distinct real-time PCR protocols have recently been published for identification of E. histolytica and differentiation from the morphologically identical nonpathogenic Entamoeba dispar. In this study, we compared three E. histolytica real-time PCR techniques published by December 2004. The limits of detection and efficiency of each real-time PCR assay were determined using DNA extracted from stool samples spiked with serially diluted cultured E. histolytica trophozoites. The ability of each assay to correctly distinguish E. histolytica from E. dispar was evaluated with DNA extracted from patients' stools and liver aspirates submitted for confirmatory diagnosis. Real-time PCR allowed quantitative analysis of the spiked stool samples, but major differences in detection limits and assay performance were observed among the evaluated tests. These results illustrate the usefulness of comparative evaluations of diagnostic assays.
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Affiliation(s)
- Yvonne Qvarnstrom
- National Center for Infectious Diseases, Centers for Disease Control and Prevention, Public Health Service, U.S. Department of Health and Human Services, Atlanta, Georgia 30341, USA
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Abstract
The detection of Entamoeba histolytica, the causative agent of amebiasis, is an important goal of the clinical microbiology laboratory. To assess the scope of E. histolytica infection, it is necessary to utilize accurate diagnostic tools. As more is discovered about the molecular and cell biology of E. histolytica, there is great potential for further understanding the pathogenesis of amebiasis. Molecular biology-based diagnosis may become the technique of choice in the future because establishment of these protozoa in culture is still not a routine clinical laboratory process. In all cases, combination of serologic tests with detection of the parasite (by antigen detection or PCR) offers the best approach to diagnosis, while PCR techniques remain impractical in many developing country settings. The detection of amebic markers in serum in patients with amebic colitis and liver abscess appears promising but is still only a research tool. On the other hand, stool antigen detection tests offer a practical, sensitive, and specific way for the clinical laboratory to detect intestinal E. histolytica. All the current tests suffer from the fact that the antigens detected are denatured by fixation of the stool specimen, limiting testing to fresh or frozen samples.
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Affiliation(s)
- Mehmet Tanyuksel
- Department of Microbiology and Clinical Microbiology, Gulhane Military Medical Academy, Etlik, Ankara 06018, Turkey
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Ghosh S, Satish S, Tyagi S, Bhattacharya A, Bhattacharya S. Differential use of multiple replication origins in the ribosomal DNA episome of the protozoan parasite Entamoeba histolytica. Nucleic Acids Res 2003; 31:2035-44. [PMID: 12682354 PMCID: PMC153748 DOI: 10.1093/nar/gkg320] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The factors that control the initiation of eukaryotic DNA replication from defined origins (oris) on the chromosome remain incompletely resolved. Here we show that the circular rDNA episome of the human pathogen Entamoeba histolytica contains multiple potential oris, which are utilized in a differential manner. The primary ori in exponentially growing cells was mapped close to the promoter of rRNA genes in the upstream intergenic spacer (IGS) by two-dimensional gel electrophoresis. Replication initiated predominantly from the upstream IGS and terminated in the downstream IGS. However, when serum-starved cells were allowed to resume growth, the early oris which became activated were located in other parts of the molecule. Later the ori in the upstream IGS became activated, with concomitant silencing of the early oris. When the upstream IGS was located ectopically in an artificial plasmid, it again lost ori activity, while other parts of the rDNA episome could function as oris in this system. Therefore, the activation or silencing of the ori in this episome is context dependent, as is also the case with many eukaryotic replicons. This is the first replication origin to be mapped in this primitive protozoan and will provide an opportunity to define the factors involved in differential ori activity, and their comparison with metazoans.
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Affiliation(s)
- Soma Ghosh
- School of Life Sciences, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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Blessmann J, Buss H, Nu PAT, Dinh BT, Ngo QTV, Van AL, Abd Alla MD, Jackson TFHG, Ravdin JI, Tannich E. Real-time PCR for detection and differentiation of Entamoeba histolytica and Entamoeba dispar in fecal samples. J Clin Microbiol 2002; 40:4413-7. [PMID: 12454128 PMCID: PMC154634 DOI: 10.1128/jcm.40.12.4413-4417.2002] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A closed-tube, real-time PCR assay was developed for sensitive and specific detection and differentiation of the two closely related intestinal protozoan parasites Entamoeba histolytica and Entamoeba dispar directly from human feces. The assay is performed with the LightCycler system using fluorescence-labeled detection probes and primers amplifying a 310-bp fragment from the high-copy-number, ribosomal DNA-containing ameba episome. The assay was able to detect as little as 0.1 parasite per g of feces. The two pairs of primers used were specific for the respective ameba species, and results were not influenced by the presence of other Entamoeba species even when present in exceeding amounts. PCR was evaluated using several hundred stool samples from areas of amebiasis endemicity in Vietnam and South Africa, and results were compared with those of microscopy and ameba culture. PCR was found to be significantly more sensitive than microscopy or culture, as all samples positive by microscopy and 22 out of 25 (88%) samples positive by culture were also positive by PCR, but PCR revealed a considerable number of additional E. histolytica- or E. dispar-positive samples. Compared to culture and subsequent ameba differentiation by isoenzyme analysis, PCR was 100% specific for each of the two Entamoeba species. Interestingly, the comparison with PCR revealed that culture, in particular, underestimates E. histolytica infections. Given the high sensitivity and specificity of the developed PCR assay, the inability of microscopy to distinguish between the two ameba species, and the time it takes to culture and subsequently differentiate entamoebae by isoenzyme analysis, this assay is more suitable than microscopy or culture to correctly diagnose intestinal E. histolytica or E. dispar infection.
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Affiliation(s)
- Joerg Blessmann
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Medical College, Hué, Vietnam, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, Medical Research Council (Natal), Congella, South Africa
| | - Heidrun Buss
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Medical College, Hué, Vietnam, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, Medical Research Council (Natal), Congella, South Africa
| | - Phuong A. Ton Nu
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Medical College, Hué, Vietnam, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, Medical Research Council (Natal), Congella, South Africa
| | - Binh T. Dinh
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Medical College, Hué, Vietnam, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, Medical Research Council (Natal), Congella, South Africa
| | - Quynh T. Viet Ngo
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Medical College, Hué, Vietnam, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, Medical Research Council (Natal), Congella, South Africa
| | - An Le Van
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Medical College, Hué, Vietnam, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, Medical Research Council (Natal), Congella, South Africa
| | - Mohamed D. Abd Alla
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Medical College, Hué, Vietnam, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, Medical Research Council (Natal), Congella, South Africa
| | - Terry F. H. G. Jackson
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Medical College, Hué, Vietnam, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, Medical Research Council (Natal), Congella, South Africa
| | - Jonathan I. Ravdin
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Medical College, Hué, Vietnam, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, Medical Research Council (Natal), Congella, South Africa
| | - Egbert Tannich
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Medical College, Hué, Vietnam, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, Medical Research Council (Natal), Congella, South Africa
- Corresponding author. Mailing address: Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany. Phone: 49-40-42818-477. Fax: 49-40-42818-512. E-mail:
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40
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Close sequence identity between ribosomal DNA episomes of the non-pathogenicEntamoeba dispar and pathogenicEntamoeba histolytica. J Biosci 2002. [DOI: 10.1007/bf02704857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ghosh S, Zaki M, Clark CG, Bhattacharya S. Recombinational loss of a ribosomal DNA unit from the circular episome of Entamoeba histolytica HM-1:IMSS. Mol Biochem Parasitol 2001; 116:105-8. [PMID: 11463474 DOI: 10.1016/s0166-6851(01)00305-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- S Ghosh
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
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Orozco E, Gómez C, Pérez DG, García-Rivera G, Sánchez T, Bañuelos C, Mendoza L, Solís F, Gómez E, Ramos R, Flores E. Entamoeba histolytica hybrids. Arch Med Res 2000; 31:S273-4. [PMID: 11070313 DOI: 10.1016/s0188-4409(00)00189-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- E Orozco
- Departamento de Patología Experimental, Centro de Investigación y de Estudios Avanzados del I.P.N. (Cinvestav), Mexico City, Mexico.
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43
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Abstract
Estimation of genome size of Entamoeba histolytica by different methods has failed to give comparable values due to the inherent complexities of the organism, such as the uncertain level of ploidy, presence of multinucleated cells and a poorly demarcated cell division cycle. The genome of E. histolytica has a low G+C content (22.4%), and is composed of both linear chromosomes and a number of circular plasmid-like molecules. The rRNA genes are located exclusively on some of the circular DNAs. Karyotype analysis by pulsed field gel electrophoresis suggests the presence of 14 conserved linkage groups and an extensive size variation between homologous chromosomes from different isolates. Several repeat families have been identified, some of which have been shown to be present in all the electrophoretically separated chromosomes. The typical nucleosomal structure has not been demonstrated, though most of the histone genes have been identified. Most Entamoeba genes lack introns, have short 3' and 5' untranslated regions, and are tightly packed. Promoter analysis revealed the presence of three conserved motifs and several upstream regulatory elements. Unlike typical eukaryotes, the transcription of protein coding genes is alpha-amanitin resistant. Expressed Sequence Tag analysis has identified a group of highly abundant polyadenylated RNAs which are unlikely to be translated. The Expressed Sequence Tag approach has also helped identify several important genes which encode proteins that may be involved in different biochemical pathways, signal transduction mechanisms and organellar functions.
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Affiliation(s)
- A Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, India.
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44
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Willhoeft U, Tannich E. Fluorescence microscopy and fluorescence in situ hybridization of Entamoeba histolytica nuclei to analyse mitosis and the localization of repetitive DNA. Mol Biochem Parasitol 2000; 105:291-6. [PMID: 10693751 DOI: 10.1016/s0166-6851(99)00181-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- U Willhoeft
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.
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45
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Bagchi A, Bhattacharya A, Bhattacharya S. Lack of a chromosomal copy of the circular rDNA plasmid of Entamoeba histolytica. Int J Parasitol 1999; 29:1775-83. [PMID: 10616923 DOI: 10.1016/s0020-7519(99)00125-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A number of small circular DNAs constitute a part of the genome of Entamoeba histolytica. Among them, the 24.5 kb circular DNA encoding rRNA (EhR1) is the most abundant. Pulsed field gel electrophoresis was used to determine if a chromosomal copy of EhR1 exists and what fraction of the total genome is circular. The results show that the chromosomes of E. histolytica are linear, and that no copy of EhR1 could be detected in any of the linear chromosomes.
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Affiliation(s)
- A Bagchi
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
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46
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Abstract
Although knowledge about gene organization and transcription control in the protozoan parasite Entamoeba histolytica has increased substantially during the last few years, questions remain open about ploidy, organization and number of chromosomes in this human pathogen. To get insight into these questions conditions were elaborated to consistently separate E. histolytica chromosomes using pulsed-field gel electrophoresis. Southern blot analyses indicated variations in number and size of homologous chromosomes between various E. histolytica isolates, but only minor differences were observed between clones of a given isolate. Depending on the isolate used 31-35 chromosomes were identified ranging in size from 0.3 to 2.2 megabases. The assignment of 68 independent cDNA probes to the chromosomes of three axenically cultured E. histolytica isolates identified 14 linkage groups, which suggested a haploid genome-size of < or =20 megabases. As single copy probes bound to as many as four chromosome-sized bands, it is most likely that E. histolytica has a functional ploidity of at least 4.
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Affiliation(s)
- U Willhoeft
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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47
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Willhoeft U, Buss H, Tannich E. Analysis of cDNA expressed sequence tags from Entamoeba histolytica: identification of two highly abundant polyadenylated transcripts with no overt open reading frames. Protist 1999; 150:61-70. [PMID: 10724519 DOI: 10.1016/s1434-4610(99)70009-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Upon analysis of 304 expressed sequence tags derived from the protozoan parasite Entamoeba histolytica, a number of novel protein encoding amoeba sequences were isolated. In addition, two unrelated, abundantly expressed transcripts were identified, and designated, ehapt1 and ehapt2. Although these transcripts do not contain any overt open reading frame, both are polyadenylated and together represent about 19% of total polyA+-RNA(11.6% for ehapt1 and 7.5% for ehapt2), thus being the most highly expressed polyA-containing transcripts so far identified in E. histolytica trophozoites. Northern blot and primer extension analyses revealed single-sized transcripts of 0.5 and 0.6 kb for ehapt1 and ehapt2, respectively, and Southern blot analysis suggests that both are encoded by multiple genes, which are distributed throughout the amoeba genome. Comparison between various ehapt1- and ehapt2-derived cDNAs indicated that both transcripts are highly polymorphic. Whereas nucleotide substitutions in ehapt2 are distributed throughout the sequence, variations in ehapt1 are mainly restricted to two regions, one of which comprises a deletion of variable length within an 8 nt tandem repeat unit. At present there is no convincing explanation for the possible role of ehapt1 and ehapt2 in E. histolytica, and analogous sequences have not been described so far for any other organism. Most likely they might represent regulatory RNAs or transcribed transposable elements.
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Affiliation(s)
- U Willhoeft
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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