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    The impact of including tRNA content on the optimality of the genetic code

    , Article Bulletin of Mathematical Biology ; Volume 67, Issue 6 , 2005 , Pages 1355-1368 ; 00928240 (ISSN) Goodarzi, H ; Shateri Najafabadi, H ; Ahmadi Nejad, H ; Torabi, N ; Sharif University of Technology
    2005
    Abstract
    Statistical and biochemical studies have revealed nonrandom patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslational errors and point mutations, since it is known that, when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, we have taken into consideration both relative frequencies of amino acids and relative gene copy frequencies of tRNAs in genomic sequences in order to introduce a fitness function which models the mistranslational probabilities more accurately in modern organisms. The... 

    Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach

    , Article Journal of Bioinformatics and Computational Biology ; Volume 13, Issue 2 , April , 2015 ; 02197200 (ISSN) Foroughmand Araabi, M. H ; Goliaei, B ; Alishahi, K ; Sadeghi, M ; Goliaei, S ; Sharif University of Technology
    World Scientific Publishing Co. Pte Ltd  2015
    Abstract
    Although it is known that synonymous codons are not chosen randomly, the role of the codon usage in gene regulation is not clearly understood, yet. Researchers have investigated the relation between the codon usage and various properties, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Recently, a universal codon usage based mechanism for gene regulation is proposed. We studied the role of protein sequence patterns on the codons usage by related genes. Considering a subsequence of a protein that matches to a pattern or motif, we showed that, parts of the genes, which are translated to this subsequence, use specific ratios of... 

    Dependency of codon usage on protein sequence patterns: A statistical study

    , Article Theoretical Biology and Medical Modelling ; Vol. 11, issue. 1 , 2014 ; ISSN: 17424682 Foroughmand-Araabi, M. H ; Goliaei, B ; Alishahi, K ; Sadeghi, M ; Sharif University of Technology
    Abstract
    Background: Codon degeneracy and codon usage by organisms is an interesting and challenging problem. Researchers demonstrated the relation between codon usage and various functions or properties of genes and proteins, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Researchers usually represent segments of proteins responsible for specific functions or structures in a family of proteins as sequence patterns or motifs. We asked the question if organisms use the same codons in pattern segments as compared to the rest of the sequence. Methods. We used the likelihood ratio test, Pearson's chi-squared test, and mutual information... 

    A quantum mechanical approach towards the calculation of transition probabilities between DNA codons

    , Article BioSystems ; Volume 184 , 2019 ; 03032647 (ISSN) Ghasemi, F ; Shafiee, A ; Sharif University of Technology
    Elsevier Ireland Ltd  2019
    Abstract
    The role of quantum tunneling in altering the structure of nucleotides to each other and causing a mutational event in DNA has been a topic of debate for years. Here, we introduce a new quantum mechanical approach for analyzing a typical point-mutation in DNA strands. Assuming each codon as a base state, a superposition of codon states could provide a physical description for a set of codons encoding the same amino acid and there are transition amplitudes between them. We choose the amino acids Phe and Ile as our understudy bio-systems which are encoded by two and three codons, respectively. We treat them as large quantum systems and use double- and triple-well potential models to study the... 

    On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices

    , Article Journal of Theoretical Biology ; Volume 235, Issue 3 , 2005 , Pages 318-325 ; 00225193 (ISSN) Goodarzi, H ; Shateri Najafabadi, H ; Hassani, K ; Ahmadi Nejad, H ; Torabi, N ; Sharif University of Technology
    2005
    Abstract
    Statistical and biochemical studies have revealed non-random patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslation errors and point mutations, since it is known that when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, using altered forms of the fitness functions used in the prior studies, we have optimized the parameters involved in the calculation of the error minimizing property of the genetic code so that the genetic code outscores the random codes as much as possible. This work also... 

    Homozygous mutations in C14orf39/SIX6OS1 cause non-obstructive azoospermia and premature ovarian insufficiency in humans

    , Article American Journal of Human Genetics ; Volume 108, Issue 2 , 2021 , Pages 324-336 ; 00029297 (ISSN) Fan, S ; Jiao, Y ; Khan, R ; Jiang, X ; Javed, A. R ; Ali, A ; Zhang, H ; Zhou, J ; Naeem, M ; Murtaza, G ; Li, Y ; Yang, G ; Zaman, Q ; Zubair, M ; Guan, H ; Zhang, X ; Ma, H ; Jiang, H ; Ali, H ; Dil, S ; Shah, W ; Ahmad, N ; Zhang, Y ; Shi, Q ; Sharif University of Technology
    Cell Press  2021
    Abstract
    Human infertility is a multifactorial disease that affects 8%–12% of reproductive-aged couples worldwide. However, the genetic causes of human infertility are still poorly understood. Synaptonemal complex (SC) is a conserved tripartite structure that holds homologous chromosomes together and plays an indispensable role in the meiotic progression. Here, we identified three homozygous mutations in the SC coding gene C14orf39/SIX6OS1 in infertile individuals from different ethnic populations by whole-exome sequencing (WES). These mutations include a frameshift mutation (c.204_205del [p.His68Glnfs∗2]) from a consanguineous Pakistani family with two males suffering from non-obstructive...