Search results for " Codon"
showing 10 items of 75 documents
Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals
2000
The study of a few genes has permitted the identification of three elements that constitute a yeast polyadenylation signal: the efficiency element (EE), the positioning element and the actual site for cleavage and polyadenylation. In this paper we perform an analysis of oligonucleotide composition on the sequences located downstream of the stop codon of all yeast genes. Several oligonucleotide families appear over-represented with a high significance (referred to herein as"words"). The family with the highest over-representation includes the oligonucleotides shown experimentally to play a role as EEs. The word with the highest score is TATATA, followed, among others, by a series of singl…
Cloning and sequencing of the dnaK region of Streptomyces coelicolor A3(2)
1993
Abstract The dnaK homologue of Streptomyces coelicolor A3(2) strain M145 has been cloned and sequenced. Nucleotide sequence analysis of a 2.5-kb region revealed an open reading frame (ORF) encoding a predicted DnaK protein of 618 amino acids (Mr = 66 274). The dnaK coding sequence displays extreme codon bias and shows a strong preference for CGY and GGY, for Arg and Gly codons, respectively. The predicted DnaK sequence has a high Lys:Arg ratio which is not typical of streptomycete proteins. The region immediately downstream from dnaK contains an ORF for a GrpE-like protein; the predicted start codon of grpE overlaps the last two codons of dnaK, indicating that the two genes are translationa…
Taxonomic investigation on Allium hirtovaginum group (Amaryllidaceae) from East Mediterranean area
2021
Within taxonomic studies on Allium sect. Codonoprasum from Mediterranean flora, populations belonging to A. hirtovaginum Candargy group were examined. Based on field investigation and herbarium surveyes, this group is represented by very critical and not well known taxa, distributed in the East Mediterranean, showing a marked morphological variability. Currently, the species referable to this group in addition to A. hirtovaginum are also A. pilosum Sibth. & Sm., A. aeginiense Brullo, Giusso & Terrasi and A. nerimaniae Koçyiğit & Kaya. Besides, other 13 species are here described as new to science, they are A. pythagoricum, A. pignattii, A. hippocraticum, A. abanticum, A. velutin…
Nonsense codons suppression. An acute toxicity study of three optimized TRIDs in murine model, safety and tolerability evaluation.
2022
Stop mutations cause 11% of the genetic diseases, due to the introduction of a premature termination codon (PTC) in the mRNA, followed by the production of a truncated protein. A promising therapeutic approach is the suppression therapy by Translational Readthrough Inducing Drugs (TRIDs), restoring the expression of the protein. Recently, three new TRIDs (NV848, NV914, NV930) have been proposed, and validated by several in vitro assays, for the rescue of the CFTR protein, involved in Cystic Fibrosis disease. In this work, an acute toxicological study for the three TRIDs was conducted in vivo on mice, according to the OECD No.420 guidelines. Animals were divided into groups and treated with …
Heterozygous nonsense SCN5A mutation W822X explains a simultaneous sudden infant death syndrome.
2008
The sudden, unexpected, and unexplained death of both members of a set of healthy twins (simultaneous sudden infant death syndrome (SSIDS)) is defined as a case in which both infants meet the definition of sudden infant death syndrome individually. A search of the world medical literature resulted in only 42 reported cases of SSIDS. We report the case of a pair of identical, male, monozygotic twins, 138 days old, who suddenly died, meeting the full criteria of SSIDS and where a genetic screen was performed, resulting in a heterozygous nonsense SCN5A mutation (W822X) in both twins. Immunohistochemistry was performed on cardiac tissue samples utilizing polyclonal antibodies anti-Na+ CP type V…
Identification and validation of novel molecules obtained by integrated computational and experimental approaches for the read-through of PTCs in CF …
2015
Deciphering the Nonsense Readthrough Mechanism of Action of Ataluren: An in Silico Compared Study
2019
Ataluren was reported to suppress nonsense mutations by promoting the readthrough of premature stop codons, although its mechanism of action (MOA) is still debated. The likely interaction of Ataluren with CFTR-mRNA has been previously studied by molecular dynamics. In this work we extended the modeling of Ataluren's MOA by complementary computational approaches such as induced fit docking (IFD), quantum polarized ligand docking (QPLD), MM-GBSA free-energy calculations, and computational mutagenesis. In addition to CFTR-mRNA, this study considered other model targets implicated in the translation process, such as eukaryotic rRNA 18S, prokaryotic rRNA 16S, and eukaryotic Release Factor 1 (eRF…
Stop codon insertion restores the particle formation ability of hepatitis B virus core-hantavirus nucleocapsid protein fusions.
2003
In recent years, epitopes of various origin have been inserted into the core protein of hepatitis B virus (HBc), allowing the formation of chimeric HBc particles. Although the C-terminus of a C-terminally truncated HBc (HBcΔ) tolerates the insertion of extended foreign sequences, the insertion capacity is still a limiting factor for the construction of multivalent vaccines. Previously, we described a new system to generate HBcΔ mosaic particles based on a read-through mechanism in an <i>Escherichia coli</i> suppressor strain [J Gen Virol 1997;78:2049–2053]. Those mosaic particles allowed the insertion of a 114-amino acid (aa)-long segment of a Puumala hantavirus (PUUV) nucleocap…
Analisi molecolare e filogenesi delle specie a fioritura tardiva del genere Allium (Alliaceae)
2014
Questo contributo presenta i risultati di uno studio di filogenesi molecolare sulla sez. Codonoprasum, con particolare riferimento alle specie a fioritura autunnale. Per confronto sono state inserite le specie a fioritura tardiva di altri sottogeneri e sezioni, insieme ad altri taxa non tardivi della sez. Codonoprasum e di altre sezioni filogeneticamente più affini. Le analisi sono state svolte con marcatori nucleari (ITS) e plastidiali (trnL-trnF, trnH-psbA) su un totale di 66 accessioni, utilizzano i metodi di massima parsimonia e inferenza bayesiana.
Enhancement of premature stop codon readthrough in the CFTR gene by Ataluren (PTC124) derivatives.
2015
Abstract Premature stop codons are the result of nonsense mutations occurring within the coding sequence of a gene. These mutations lead to the synthesis of a truncated protein and are responsible for several genetic diseases. A potential pharmacological approach to treat these diseases is to promote the translational readthrough of premature stop codons by small molecules aiming to restore the full-length protein. The compound PTC124 (Ataluren) was reported to promote the readthrough of the premature UGA stop codon, although its activity was questioned. The potential interaction of PTC124 with mutated mRNA was recently suggested by molecular dynamics (MD) studies highlighting the importanc…