keyword
MENU ▼
Read by QxMD icon Read
search

codon bias

keyword
https://www.readbyqxmd.com/read/28549175/selfing-in-haploid-plants-and-efficacy-of-selection-codon-usage-bias-in-the-model-moss-physcomitrella-patens
#1
Péter Szövényi, Kristian K Ullrich, Stefan A Rensing, Daniel Lang, Nico van Gessel, Hans K Stenøien, Elena Conti, Ralf Reski
Long term reduction in effective population size will lead to major shift in genome evolution. In particular, when effective population size is small, genetic drift becomes dominant over natural selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size of populations. Theory predicts that this reduction should be more dramatic in organisms capable for haploid than for diploid selfing. Although theoretically well-grounded, this assertion received mixed experimental support...
May 26, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28545477/optimizing-complex-phenotypes-through-model-guided-multiplex-genome-engineering
#2
Gleb Kuznetsov, Daniel B Goodman, Gabriel T Filsinger, Matthieu Landon, Nadin Rohland, John Aach, Marc J Lajoie, George M Church
We present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide mutations that recover 59% of the fitness defect exhibited by the 63-codon E. coli strain C321.∆A. By introducing targeted combinations of changes in multiplex we generate rich genotypic and phenotypic diversity and characterize clones using whole-genome sequencing and doubling time measurements. Regularized multivariate linear regression accurately quantifies individual allelic effects and overcomes bias from hitchhiking mutations and context-dependence of genome editing efficiency that would confound other strategies...
May 25, 2017: Genome Biology
https://www.readbyqxmd.com/read/28543534/a-chimeric-protein-of-cfa-i-cs6-subunits-and-ltb-sta-toxoid-could-protect-immunized-mice-against-enterotoxigenic-escherichia-coli
#3
Narges Zeinalzadeh, Ali Hatef Salmanian, Goli Goujani, Jafar Amani, Ghasem Ahangari, Asal Akhavian, Mahyat Jafari
Enterotoxigenic Escherichia Coli (ETEC) strains are the most common bacteria causing diarrhea in children in developing countries and travelers to these areas. Colonization factors (CFs) and enterotoxins are the main virulence determinants in ETEC pathogenesis. Heterogeneity of CFs commonly considered as the bottleneck to achieve an effective vaccine. On the other hand, it is believed that a broad spectrum protection against ETEC would be available when the anti-CF and anti-enterotoxin immunity were induced simultaneously...
May 23, 2017: Microbiology and Immunology
https://www.readbyqxmd.com/read/28537229/-genomics-and-transcriptomics-of-the-chinese-liver-fluke-clonorchis-sinensis-opisthorchiidae-trematoda
#4
G N Chelomina
The review summarizes the results of first genomic and transcriptomic investigations of the liver fluke Clonorchis sinensis (Opisthorchiidae, Trematoda). The studies mark the dawn of the genomic era for opisthorchiids, which cause severe hepatobiliary diseases in humans and animals. Their results aided in understanding the molecular mechanisms of adaptation to parasitism, parasite survival in mammalian biliary tracts, and genome dynamics in the individual development and the development of parasite-host relationships...
March 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28533334/the-evolutionary-basis-of-translational-accuracy-in-plants
#5
Salvatore Camiolo, Gaurav Sablok, Andrea Porceddu
Mistranslation errors compromise fitness by wasting resources on nonfunctional proteins. In order to reduce the cost of mistranslations, natural selection chooses the most accurately-translated codons at sites that are particularly important for protein structure and function. We investigated the determinants underlying selection for translational accuracy in several species of plants belonging to three clades: the Brassicaceae, Fabidae and Poaceae. Although signatures of translational selection were found in genes from a wide range of species, the underlying factors varied in nature and intensity...
May 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28531201/evolutionary-forces-affecting-synonymous-variations-in-plant-genomes
#6
Yves Clément, Gautier Sarah, Yan Holtz, Felix Homa, Stéphanie Pointet, Sandy Contreras, Benoit Nabholz, François Sabot, Laure Sauné, Morgane Ardisson, Roberto Bacilieri, Guillaume Besnard, Angélique Berger, Céline Cardi, Fabien De Bellis, Olivier Fouet, Cyril Jourda, Bouchaib Khadari, Claire Lanaud, Thierry Leroy, David Pot, Christopher Sauvage, Nora Scarcelli, James Tregear, Yves Vigouroux, Nabila Yahiaoui, Manuel Ruiz, Sylvain Santoni, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, Sylvain Glémin
Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28506040/codon-usage-patterns-of-tyrosinase-genes-in-clonorchis-sinensis
#7
Young-An Bae
Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined...
April 2017: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28486986/the-link-between-adjacent-codon-pairs-and-mrna-stability
#8
Yuriko Harigaya, Roy Parker
BACKGROUND: Evidence in diverse organisms suggests that codon optimality is a major determinant of mRNA translation and degradation. Codon optimality is thought to act by modulating the efficiency of ribosome elongation. In Saccharomyces cerevisiae, a recent study has identified 17 adjacent codon pairs that mediate strong inhibition of translation elongation. However, relationships between the inhibitory codon pairs and other aspects of gene expression are unknown. RESULTS: To gain insights into how the inhibitory codon pairs may affect aspects of gene expression, we utilized existing datasets to conduct genome-scale analyses in S...
May 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28482199/adar-deaminase-a-to-i-editing-of-dna-and-rna-moieties-of-rna-dna-hybrids-has-implications-for-the-mechanism-of-ig-somatic-hypermutation
#9
Edward J Steele, Robyn A Lindley
The implications are discussed of recently published biochemical studies on ADAR-mediated A-to-I DNA and RNA deamination at RNA:DNA hybrids. The significance of these data are related to previous work on strand-biased and codon-context mutation signatures in B lymphocytes and cancer genomes. Those studies have established that there are two significant strand biases at A:T and G:C base pairs, A-site mutations exceed T-site mutations (A>T) by 2.9 fold and G-site mutations exceed C-site mutations (G>C) by 1...
April 21, 2017: DNA Repair
https://www.readbyqxmd.com/read/28449301/the-profile-and-dynamics-of-rna-modifications-in-animals
#10
Pieter van Delft, Alper Akay, Sabrina M Huber, Christoph Bueschl, Konrad L M Rudolph, Tomás Di Domenico, Rainer Schuhmacher, Eric A Miska, Shankar Balasubramanian
More than a hundred distinct modified nucleosides have been identified in RNA, but little is known about their distribution across different organisms, their dynamic nature and their response to cellular and environmental stress. Mass-spectrometry-based methods have been at the forefront of identifying and quantifying modified nucleosides. However, they often require synthetic reference standards, which do not exist in the case of many modified nucleosides, and this therefore impedes their analysis. Here we use a metabolic labelling approach to achieve rapid generation of bio-isotopologues of the complete Caenorhabditis elegans transcriptome and its modifications and use them as reference standards to characterise the RNA modification profile in this multicellular organism through an untargeted liquid-chromatography tandem high-resolution mass spectrometry (LC-HRMS) approach...
March 16, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28449100/integrated-analysis-of-individual-codon-contribution-to-protein-biosynthesis-reveals-a-new-approach-to-improving-the-basis-of-rational-gene-design
#11
Juan C Villada, Otávio José Bernardes Brustolini, Wendel Batista da Silveira
Gene codon optimization may be impaired by the misinterpretation of frequency and optimality of codons. Although recent studies have revealed the effects of codon usage bias (CUB) on protein biosynthesis, an integrated perspective of the biological role of individual codons remains unknown. Unlike other previous studies, we show, through an integrated framework that attributes of codons such as frequency, optimality and positional dependency should be combined to unveil individual codon contribution for protein biosynthesis...
April 24, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28448468/transcriptome-analysis-of-core-dinoflagellates-reveals-a-universal-bias-towards-gc-rich-codons
#12
Ernest Williams, Allen Place, Tsvetan Bachvaroff
Although dinoflagellates are a potential source of pharmaceuticals and natural products, the mechanisms for regulating and producing these compounds are largely unknown because of extensive post-transcriptional control of gene expression. One well-documented mechanism for controlling gene expression during translation is codon bias, whereby specific codons slow or even terminate protein synthesis. Approximately 10,000 annotatable genes from fifteen "core" dinoflagellate transcriptomes along a range of overall guanine and cytosine (GC) content were used for codonW analysis to determine the relative synonymous codon usage (RSCU) and the GC content at each codon position...
April 27, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28427327/analysis-of-transcriptome-data-reveals-multifactor-constraint-on-codon-usage-in-taenia-multiceps
#13
Xing Huang, Jing Xu, Lin Chen, Yu Wang, Xiaobin Gu, Xuerong Peng, Guangyou Yang
BACKGROUND: Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. RESULTS: Analysis of a total of 8,620 annotated mRNA sequences from T...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28421323/gene-expression-nucleotide-composition-and-codon-usage-bias-of-genes-associated-with-human-y-chromosome
#14
Monisha Nath Choudhury, Arif Uddin, Supriyo Chakraborty
Analysis of codon usage pattern is important to understand the genetic and evolutionary characteristics of genomes. We have used bioinformatic approaches to analyze the codon usage bias (CUB) of the genes located in human Y chromosome. Codon bias index (CBI) indicated that the overall extent of codon usage bias was low. The relative synonymous codon usage (RSCU) analysis suggested that approximately half of the codons out of 59 synonymous codons were most frequently used, and possessed a T or G at the third codon position...
April 18, 2017: Genetica
https://www.readbyqxmd.com/read/28420819/synonymous-and-biased-codon-usage-by-mers-cov-papain-like-and-3cl-proteases
#15
Mahmoud Kandeel, Abdallah Altaher
Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at different sites to yield 16 nonstructural proteins. In this work, we provide evidence that MERS CoV 3CLpro and PLpro are subject to different genetic and evolutionary influences that shape the protein sequence, codon usage pattern, and codon usage bias...
April 18, 2017: Biological & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28419256/chloromitocu-codon-patterns-across-organelle-genomes-for-functional-genomics-and-evolutionary-applications
#16
Gaurav Sablok, Ting-Wen Chen, Chi-Ching Lee, Chi Yang, Ruei-Chi Gan, Jill L Wegrzyn, Nicola L Porta, Kinshuk C Nayak, Po-Jung Huang, Claudio Varotto, Petrus Tang
Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes...
April 17, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28416948/comparative-analysis-of-predicted-gene-expression-among-crenarchaeal-genomes
#17
Shibsankar Das, Brajadulal Chottopadhyay, Satyabrata Sahoo
Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416383/comparative-characterization-analysis-of-synonymous-codon-usage-bias-in-classical-swine-fever-virus
#18
Xin Xu, Dongliang Fei, Huansheng Han, Honggui Liu, Jiayong Zhang, Yulong Zhou, Chuang Xu, Hongbin Wang, Hongwei Cao, Hua Zhang
Classical swine fever virus (CSFV) is responsible for the highly contagious viral disease of swine, and causes great economic loss in the swine-raising industry. Considering the significance of CSFV, a systemic analysis was performed to study its codon usage patterns. In this study, using the complete genome sequences of 76 CSFV representing three genotypes, we firstly analyzed the relative nucleotide composition, effective number of codon (ENC) and synonymous codon usage in CSFV genomes. The results showed that CSFV is GC-moderate genome and the third-ended codons are not preferentially used...
April 14, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28401291/the-human-retinoblastoma-susceptibility-gene-rb1-an-evolutionary-story-in-primates
#19
Maria C Viana, William C Tavares, Ayslan C Brant, Mariana Boroni, Héctor N Seuánez
The tumor suppressor gene RB1 (Human Retinoblastoma Susceptibility Gene) plays a prominent role in normal development, gene transcription, DNA replication, repair, and mitosis. Its complete biallelic dysfunction in retinoblasts is the main cause of retinoblastoma in the human. Although this gene has been evolutionary conserved, comparisons between the reference and human RB1 coding region with its counterparts in 19 non-human primates showed 359 sites where nucleotide replacements took place during the radiation of these species...
April 11, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28389662/frequent-gu-wobble-pairings-reduce-translation-efficiency-in-plasmodium-falciparum
#20
Sherwin Chan, Jun-Hong Ch'ng, Mats Wahlgren, Jessada Thutkawkorapin
Plasmodium falciparum genome has 81% A+T content. This nucleotide bias leads to extreme codon usage bias and culminates in frequent insertion of asparagine homorepeats in the proteome. Using recodonized GFP sequences, we show that codons decoded via G:U wobble pairing are suboptimal codons that are negatively associated to protein translation efficiency. Despite this, one third of all codons in the genome are GU wobble codons, suggesting that codon usage in P. falciparum has not been driven to maximize translation efficiency, but may have evolved as translational regulatory mechanism...
April 7, 2017: Scientific Reports
keyword
keyword
52406
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"