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سومین کنفرانس زیست‌شناسی سامانه‌های ایران ؛ 8 و 9 اسفند ماه 1396
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| عنوان فارسی |
الگوریتم EMARI: جستجوگر متابولیتها و واکنشهای مرتبط موثر برای افزایش بازدهی تولید محصولات بیوشیمیایی |
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| چکیده فارسی مقاله |
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| عنوان انگلیسی |
EMARI: Effective Metabolites and Accompanying Reactions Identifier, a proficient algorithm to find operative routes for growth-coupled synthesis of biochemicals |
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| چکیده انگلیسی مقاله |
Objective and background Genome-scale metabolic network reconstructions (GENREs) and constraint-based genome-scale models (GEMs) as their operative mathematical representations, are proper tools in systems biology. They have been widely used to study the physiological properties of organisms and systems-based analyses of metabolism (Lewis et al., 2012) {Lewis, 2012 #4}(Yen et al., 2015). Recent in silico algorithms for classifying the pivotal genes and the associated reactions play significant roles in systems metabolic engineering (Lee et al., 2012) One of the most operative approaches for navigating the fluxes in metabolic networks to synthesize the biochemicals of interest is FBrAtio (McAnulty et al., 2012). This technique contributes to overproduction of the favorite compounds via regulating the fluxes and applying flux ratios on critical routes (pathways). Nonetheless, identifying the most effective nodes (metabolites) and edges (reactions) associated with these pathways still relies on experimental records and an appropriate approach for the relevant in silico examinations has not yet been developed. The current study presents a proficient bottom-up in silico algorithm called EMARI (Effective Metabolites and Accompanying Reactions Identifier) which identifies the effective routes to be regulated employing GEMs rather than experimental data. We used EMARI for isobutanol overproduction in Saccharomyces cerevisiae (aerobic condition) and succinate biosynthesis improvement in Escherichia coli (anaerobic condition). According to the prime outcomes provided by EMARI algorithm, growth-coupled production of the aforementioned bioproducts got possible only via regulation of at most two operational reaction fluxes. |
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| کلیدواژه‌های انگلیسی مقاله |
EMARI، Genome-scale models، Flux ratio، Constrained-based modeling، Systems biology |
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| نویسندگان مقاله |
پیام ستوده | payam setoodeh
shiraz university
دانشگاه شیراز
سازمان اصلی تایید شده: دانشگاه شیراز (Shiraz university)
فرید زارع | farid zare
shiraz university
دانشگاه شیراز
سازمان اصلی تایید شده: دانشگاه شیراز (Shiraz university)
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| نشانی اینترنتی |
http://icsb2018.modares.ac.ir/browse.php?a_code=A-10-138-1&slc_lang=fa&sid=1 |
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| زبان مقاله منتشر شده |
en |
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