Computational regulatory model for detoxification of ammonia from urea cycle in liver

A nondeterministic finite automaton was designed to monitor enzymatic regulation and detoxification of excess ammonia in the urea cycle and its disorders. The designed machine is used for the diagnosis of deficiency and for regulating the expression of any of the enzymes involved with acceptance and rejection states in the urea cycle. The urea cycle is the metabolism of excess nitrogen produced by the breakdown of protein and other nitrogen-containing molecules in liver. Disorder in the urea cycle may lead to the accumulation of toxic ammonia in the blood, which leads to hyperammonemia. The elevation of plasma ammonia concentration may ultimately lead to cerebral edema in infants and severe brain damage due to the toxicity of ammonia. The diagnosis of urea cycle disorder is based on evaluation of clinical, biochemical, and molecular data. In this study, a new therapeutic approach for urea cycle disorders is developed based on a computational model. It is used to observe the normal process of the cycle through the state of acceptance. The state of rejection denotes a deficiency in the respective enzymatic activity. Subsequently, it assists in the creation of targeted treatment for brain damage and related enzymatic deficiency disorders.

Computational regulatory model for detoxification of ammonia from urea cycle in liver

A nondeterministic finite automaton was designed to monitor enzymatic regulation and detoxification of excess ammonia in the urea cycle and its disorders. The designed machine is used for the diagnosis of deficiency and for regulating the expression of any of the enzymes involved with acceptance and rejection states in the urea cycle. The urea cycle is the metabolism of excess nitrogen produced by the breakdown of protein and other nitrogen-containing molecules in liver. Disorder in the urea cycle may lead to the accumulation of toxic ammonia in the blood, which leads to hyperammonemia. The elevation of plasma ammonia concentration may ultimately lead to cerebral edema in infants and severe brain damage due to the toxicity of ammonia. The diagnosis of urea cycle disorder is based on evaluation of clinical, biochemical, and molecular data. In this study, a new therapeutic approach for urea cycle disorders is developed based on a computational model. It is used to observe the normal process of the cycle through the state of acceptance. The state of rejection denotes a deficiency in the respective enzymatic activity. Subsequently, it assists in the creation of targeted treatment for brain damage and related enzymatic deficiency disorders.

___

  • Altay G, Altay N, Neal D (2013). Global assessment of network inference algorithms based on available literature of gene/ protein interactions. Turk J Biol 37: 547–555.
  • Aly M, Tork S, Al-Garni S, Allam R (2013). Production and characterization of uricase from Streptomyces exfoliates UR10 isolated from farm wastes. Turk J Biol 37: 520–529.
  • Balistreri WF, Carey RG (2011). Metabolic diseases of the liver. In: Kliegman RM, Stanton BF, St Geme J, Schor N, Behrman RE, editors. Nelson Textbook of Pediatrics. 19th ed. Philadelphia, PA, USA: Saunders Elsevier.
  • Batshaw ML (1984). Hyperammonemia. Curr Probl Pediatr 14: 1–69.
  • Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E (2001). Programmable and autonomous computing machine made of biomolecules. Nature 414: 430–434.
  • Caldovic L, Morizono H, Panglao MG, Cheng SF, Packman S, Tuchman M (2003). Null mutations in the N-acetylglutamate synthase gene associated with acute neonatal disease and hyperammonemia. Hum Genet 112: 364–368.
  • Cavaliere M, Jonoska N, Yogev S (2005). Biomolecular implementation of computing devices with unbounded memory. Lect Notes Comput Sc 3384: 35–49.
  • Gebert J, Lätsch M, Pickl SW, Weber GW, Wünschiers R (2006). An algorithm to analyze stability of gene-expression patterns. Discrete Appl Math 154: 1140–1156.
  • Hopcroft JE, Ullman JD (1979). Introduction to Automata Theory, Languages, and Computation. 1st ed. Boston, MA, USA: Addison-Wesley.
  • Kari L (1997). DNA computing: the arrival of biological mathematics. Math Intell 19: 9–22.
  • Krasinski T, Sakowski S, Poplawski T (2012). Autonomous push- down automaton built on DNA. Informatica 36: 263–276.
  • Lanpher BC, Gropman A, Chapman KA, Lichter-Konecki U, Summar ML (2003). Urea cycle disorders overview [Updated 1 September 2011]. In: Pagon RA, Adam MP, Bird TD, editors. GeneReviews [Internet]. Seattle, WA, USA: University of Washington: 1993–2013. 
  • Muhammad MR, Devi GP, Selvakumar R (2013). A computational model for monitoring glycolysis process in cancer cells. J Bioinf Intell Control 2: 300–304.
  • Nowak R, Plucienniczak A (2008). Finite state automata built on DNA. Biocybern Biomed Eng 28: 3–19.
  • Selvakumar R, Muhammad MR, Devi GP (2013). Computational model for the extraction of human erythropoietin. Int J ChemTech Res 5: 2623–2629.
  • Summar M (2001). Current strategies for the management of neonatal urea cycle disorders. J Pediatr 138: S30–S39.
  • Summar M, Tuchman M (2001). Proceedings of a consensus conference for the management of patients with urea cycle disorders. J Pediatr 138: S6–S10.
  • Takiguchi M, Mori M (1995). Transcriptional regulation of genes for ornithine cycle enzymes. Biochem J 312: 649–659.
  • Tuchman M, Matsuda I, Munnich A, Malcolm S, Strautnieks S, Briede T (1995). Proportions of spontaneous mutations in males and females with ornithine transcarbamylase deficiency. Am J Med Genet A 55: 67–70.
  • Weber GW, Defterli O, Gök SZA, Kropat E (2011). Modeling, inference and optimization of regulatory networks based on time series data. Eur J Oper Res 211: 1–14.
Turkish Journal of Biology-Cover
  • ISSN: 1300-0152
  • Yayın Aralığı: Yılda 6 Sayı
  • Yayıncı: TÜBİTAK
Sayıdaki Diğer Makaleler

Effect of polyamines on in vitro anther cultures of carrot (Daucus carota L.).

Krystyna GÓRECKA, Waldemar KISZCZAK, Dorota KRZYZANOWSKA, Urszula KOWALSKA, Agata KAPUSCINSKA

Large-scale purification of a bacteriocin produced by Leuconostoc mesenteroides subsp. cremoris using diatomite calcium silicate

Halil DÜNDAR, Ömür ÇELİKBIÇAK, Bekir SALİH, Tahsin Faruk BOZOĞLU

Biodegradation of the synthetic pyrethroid insecticide α-cypermethrin by Stenotrophomonas maltophilia OG2

Özlem GÜR, Murat ÖZDAL, Ömer Faruk ALGUR

NKX3.1 binding to GPX2, QSCN6, SOD1, and SOD2 promoters contributes to antioxidant response regulation via transactivation

Bilge Debeleç BÜTÜNER, Kemal Sami KORKMAZ

Phylogenetic analysis and characterization of an alkane-degrading yeast strain isolated from oil-polluted soil

Ortansa CSUTAK, Tatiana VASSU

In vitro regeneration and conservation of the lentisk (Pistacia lentiscus L.)

İbrahim KOÇ, Ahmet ONAY, Yelda Özden ÇİFTÇİ

Biodegradation of the synthetic pyrethroid insecticide α-cypermethrin by Stenotrophomonas maltophilia OG2

Ömer Faruk ALGUR, Murat ÖZDAL, Özlem GÜR

Bacterial toxin colicin N-T domain structure changes to ordered state upon binding C-terminal domain of TolA

Yakup ULUSU, Sema Bilgin ŞENTÜRK, Fatma GEDİKLİ, Jeremy H. LAKEY, İsa GÖKÇE

Computational regulatory model for detoxification of ammonia from urea cycle in liver

Rashith Muhammad MUBARAK ALI, Poornima Devi GURUSAMY, Selvakumar RAMACHANDRAN

Biodegradation of the synthetic pyrethroid insecticide α-cypermethrin by Stenotrophomonas maltophilia OG2

Özlem GÜR, Murat ÖZDAL, Ömer Faruk ALGUR