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Analysis of variations, structures, and phylogenic characteristics of bovine leukocyte antigen DRB3 exon2 | ||
| Archives of Razi Institute | ||
| مقاله 1، دوره 72، شماره 3، آذر 2017، صفحه 147-157 اصل مقاله (1.13 M) | ||
| نوع مقاله: Original Articles | ||
| شناسه دیجیتال (DOI): 10.22092/ari.2017.111611 | ||
| نویسندگان | ||
| M. M. Ranjbar1؛ S. Ataei* 2؛ Gh. Nikbakht Brujeni3؛ S. Golabdar3 | ||
| 1Department of Viral Animal Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran | ||
| 2Department of Avian Bacterial Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran | ||
| 3Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran | ||
| چکیده | ||
| Bovine leukocyte antigen (BoLA) DRB3 is a highly polymorphic gene in major histocompatibility complex (MHC) class II that plays a central role in immune responses and production factors. As of yet, molecular and evolutionary characteristics of BoLA-DRB3.2* have not been as fully understood as human and mouse. Therefore, we attempted to analyze variability and phylogeny of BoLA-DRB3.2* and illustrate some novel practical evidence on interspecies diversity, the resistance /susceptibility points in cattle breeding, and vaccine design. Initially, BoLA-DRB3.2* alleles and orthologous exons in the selected livestock were retrieved and checked. In the next step, the secondary/tertiary structure of BoLA-DRB3.2*24 gene product was modeled and validated. Then, hypervariable regions (HVRs) of alleles were identified by hybrid approaches. In the last step, interspecies relationship, allele’s phylogeny/grouping, and estimate of average evolutionary divergence were explored. Shannon entropy variation analysis showed eight HVRs and three semi-variable regions in BoLADRB3.2* alleles. These HVRs were present in all the three sub-structures and dominantly existed in alpha helix. In addition, strong relationships and little diversity were noted in phylogenetic trees of cattle, buffaloes, sheep, and goats. Furthermore, there was some evidence on divergence of DRB3 before speciation among the mentioned species and possibility of cross prediction resistance/susceptibility alleles. Finally, DRB3 alleles were grouped into seven clusters, and older and newer alleles were identified. The results show that similar studies should be done in other animals to better understand the nature of the DRB3 attributes. | ||
| کلیدواژه‌ها | ||
| BoLA-DRB3.2؛ Cattle؛ Variation؛ modeling؛ phylogeny | ||
| عنوان مقاله [English] | ||
| آنالیز تغییرات، ساختار و خصوصیات فیلوژنیک اگزون 2 از BoLA-DRB3 درگاو | ||
| چکیده [English] | ||
| اگزون2 از BoLA-DRB3 یکژن با چند شکلی بالا در MHC کلاس 2 بوده، نقش مرکزی در پاسخهای ایمنی و فاکتورهای تولیدی دارد. تا به حال خصوصیات مولکولی و تکاملی BoLA-DRB3.2 به مانند مولکولهای معادل آن درانسانی و موشی به طور کامل درک نشده است. بنابراین آنالیز تغییرپذیری و فیلوژنی BoLA-DRB3.2 صورت گرفت و برخی یافتههای کاربردی جدید در مورد تنوع بین گونهای و حساسیت / مقاوت به بیماری، و طراحی واکسن اشاره شده است. در ابتدا آللهای BoLA-DRB3.2 و اگزونهای ارتولوگ مورد نظر از پایگاه داده استخراج و ارزیابی شد. در گام بعدی ساختار دوم و سوم BoLA-DRB3.2 مدل سازی و مورد اعتبار سنجی قرار گرفت. سپس نواحی بسیار متغیر (HVRs) با رهیافتهای هیبریدی مشخص گردیدند. در گام پایانی ارتباط بین گونهای، فیلوژنی / گروهبندی آللی و تخمین میانگین واگرایی تکاملی انجام گرفت. نتایج حاکی از وجود هشت HVR و سه ناحیه مرزی در آنالیز تغییر پذیری آنتروپی شانون بود. این HVR ها در همه تحت ساختارها وجود داشته و به شکل غالب در آلفاهلیکس مشاهده شد. در بررسی فیلوژنی نیز ارتباط تکاملی بالا و تنوع پایین بین گاو، گاومیش، گوسفند و بز به دست آمد. به علاوه این شواهد حاکی از اشتقاق DRB3 قبل از گونه زایی و امکان پیشگویی متقاطع آلل های مقاومت / حساسیت را فراهم میکند. در پایان DRB3 در 7 خوشه گروهبندی گردید و ردههای آللی قدیمیتر و جدیدتر شناسایی گردید. نتایج نشان میدهد که مطالعات مشابهای نیز میبایست در سایر حیوانات صورت گیرد تا ماهیت ویژگی های DRB3 بهتر درک شود. | ||
| کلیدواژه‌ها [English] | ||
| BoLA-DRB3.2, گاو, تغییرات, مدل سازی, فیلوژنی | ||
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