Document Details
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Document Type |
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Thesis |
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Document Title |
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GENOMIC STUDIES AND DIVERSITY PROFILING OF INTESTINE ENTAMOEBA PARASITE IN MAKKAH REGION دراسة جينومية ومظاهر التنوع في طفيليات الأمعاء من جنس انتاميبا في منطقة مكة المكرمة |
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Subject |
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faculty of science |
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Document Language |
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Arabic |
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Abstract |
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Amebiasis caused by Entamoeba histolytica parasite is among the worst gut diseases worldwide. The most commonly used approach for Entamoeba species typing up to date is the tRNA-linked Short Tandem Repeat (STR) regions of the parasite’s genome. In the present study, a new reliable, fast and easy molecular tool for species typing was developed. Also, detection of gut mycobiome signature of infected subjects in a trial is require to improve the ability to diagnose and treat this disease. DNA was isolated from fecal samples collected from infected subjects in Saudi Arabia. Two types of primer sets were compared in which the first targeted tRNA-linked STR regions, while the second was designed after multiple contig alignment of the two genomes of Entamoeba histolytica and Entamoeba dispar, using NUCmer program in aligned areas with high similarity (~90%) and difference between of ~90 bp. The selection criteria secure that designed primers should pair with both EH and ED contig sequences at homologous regions of 200-500 bp of both species except for the presence of indels that result in the recovery of amplicons of two species with different sizes. Banding patterns in the tRNA-linked STR region resulted in the occurrence of several common amplicons. We speculate that primers mismatch with regions other than the specified STR arrays of Entamoeba or with organisms other than Entamoeba existed in the fecal sample. However, the STR-based approach looked very useful in studying strain typing and parasite diversity. The results for the new approach complemented those of the STR-based approach, except that the latter failed to detect coinfected subjects. Moreover, the mycobiome results indicated that diversity of samples slightly changed due to the infection. The dendrogram tree indicated that the most common phyla in the human gut are Ascomycota, Basidiomycota and Zygomycota. Based on operational taxonomic unit (OTU) abundance, the species Pichia kudriavzevii, Candida glabrata, Saccharomyces cerevisiae of phylum Ascomycota and Rhodotorula mucilaginosa of phylum Basidiomycota were found highly abundant. Analysis based on weighted unifrac diversity distances resulted in complete separation between the two groups. The results of differential abundance indicated that a number of four phyla, six families, nine genera and ten species showed considerable changes in gut mycobiome signatures within and among groups. Overall, unclassified species of the genus Malassezia (phylum Basidiomycota) showed high abundance in infected subjects as compared with healthy subjects, while families Saccharomycetaceae and Trichocomaceae, genus Saccharomyces and species S. cerevisiae (phylum Ascomycota) showed opposite results. Linear discriminant analysis effect size (LEFSE) or (LDA) indicated that the family Saccharomycetaceae, of which Saccharomyces cerevisiae is a downstream taxon, can be a biomarker of healthy subjects that can be considered as a negative biomarker for amebiasis. In conclusion, the study provides a new approach which can be useful at the species level, while the tRNA-linked STR approach can still be a good choice for strain typing. Also, the study provides new insights into the possible use of Saccharomyces as a probiotic against amebiasis.
Keywords: Amebiasis, encystation, yeast, Crabtree effect, oxidative stress, chitin formation Species typing, strain typing, STR, amplicon, NUCmer, contig. |
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Supervisor |
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Prof. Dr. Ahmed Bahieldin |
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Thesis Type |
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Doctorate Thesis |
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Publishing Year |
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1441 AH
2020 AD |
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Co-Supervisor |
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Prof. Dr. Jamal S. M. Sabir |
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Added Date |
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Sunday, March 15, 2020 |
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Researchers
| داليا عبداللطيف ابوالجدايل | Abuljadayel, Dalia Abdulatif | Researcher | Doctorate | |
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