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codon bias

Ming-Li Wu, Qing Li, Jiang Xu, Xi-Wen Li
Background: Amomum compactum is one of the basic species of the traditional herbal medicine amomi fructus rotundus, with great pharmacology effect. The system position of A. compactum is not clear yet, and the introduction of this plant has been hindered by many plant diseases. However, the correlational molecular studies are relatively scarce. Methods: The total chloroplast (cp) DNA was extracted according to previous studies, and then sequenced by 454 GS FLX Titanium platform...
2018: Chinese Medicine
Yanci Yang, Juan Zhu, Li Feng, Tao Zhou, Guoqing Bai, Jia Yang, Guifang Zhao
Fagaceae is one of the largest and economically important taxa within Fagales. Considering the incongruence among inferences from plastid and nuclear genes in the previous Fagaceae phylogeny studies, we assess the performance of plastid phylogenomics in this complex family. We sequenced and assembled four complete plastid genomes ( Fagus engleriana, Quercus spinosa, Quercus aquifolioides , and Quercus glauca ) using reference-guided assembly approach. All of the other 12 published plastid genomes in Fagaceae were retrieved for genomic analyses (including repeats, sequence divergence and codon usage) and phylogenetic inference...
2018: Frontiers in Plant Science
Pramod Shinde, Camellia Sarkar, Sarika Jalan
The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies...
February 15, 2018: Scientific Reports
Khanh Dao Duc, Zain H Saleem, Yun S Song
The Totally Asymmetric Exclusion Process (TASEP) is a classical stochastic model for describing the transport of interacting particles, such as ribosomes moving along the messenger ribonucleic acid (mRNA) during translation. Although this model has been widely studied in the past, the extent of collision between particles and the average distance between a particle to its nearest neighbor have not been quantified explicitly. We provide here a theoretical analysis of such quantities via the distribution of isolated particles...
January 2018: Physical Review. E
Getachew Tadesse, Tesfaye S Tessema, Getenet Beyene, Abraham Aseffa
BACKGROUND: Wide-ranging evidence on the occurrence of fluoroquinolone (FQ) resistance genetic determinants in African Salmonella strains is not available. The main objectives of this study were to assess the heterogeneity, estimate pooled proportions and describe the preponderance of FQ-resistance determinants in typhoidal and non-typhoidal Salmonella (NTS) isolates of Africa. METHODS: Genetic and phenotypic data on 6103 Salmonella isolates were considered. Meta- and frequency analyses were performed depending on the number of studies by category, number of isolates and risks of bias...
2018: PloS One
Dechun Lin, Liqiang Li, Tian Xie, Qingqing Yin, Nitin Saksena, Rangke Wu, Wanyu Li, Geyang Dai, Jinmin Ma, Xiaohong Zhou, Xiao-Guang Chen
A comprehensive demonstration of Zika virus (ZIKV) molecular evolution is essential for understanding its adaptation and expansion in its recent pandemics. Despite several studies on mutations and codon usage in ZIKVs, the variations in codon usage patterns across individual genes and their biological implication remains unclear. Here, we performed a gene-by-gene comparison of the codon usage variation in ZIKVs of the African and Asian lineages. We found that besides the evidence of positive selection (Ka/Ks > 1) in the Asian lineage of the ZIKV genome, codon usage patterns were gene-specific and codon usage variation of ZIKV genes, was possibly constrained by their individual functional features, such as transmembrane domains, or antigenicity...
February 8, 2018: Virus Research
Rama K Sarvani, Drashti R Parmar, Wajeeda Tabasum, Neelima Thota, Ara Sreenivas, Ajay Gaur
The mitochondrial genome of Indian mouse deer (Moschiola indica) was sequenced, assembled and characterized for the first time using 22 pairs of polymerase chain reaction (PCR) primers. The mitogenome of M. indica which is 16,444 bp in size was found very similar to most vertebrates in organisation that harbours 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA and 1A + T-rich region. Its comparison with over 52 mitogenomes of the order Artiodactyla, showed a conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins except that M...
February 9, 2018: Scientific Reports
Arie Ryvkin, Haim Ashkenazy, Yael Weiss-Ottolenghi, Chen Piller, Tal Pupko, Jonathan M Gershoni
Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study, we implemented next generation sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon over-representation as well as in high G phosphoramidite abundance causing amino acid distribution biases...
February 6, 2018: Nucleic Acids Research
Supriyo Chakraborty, Tarikul Huda Mazumder, Arif Uddin
The BRCA1 gene is located on the human chromosome 17q21.31 and plays important role in biological processes. The aminoacyl-tRNA synthetases (AARS) are a family of heterogenous enzymes responsible protein synthesis and whose secondary functions include a role in autoimmune myositis. Our findings reveal that the compositional constraint and the preference of more A/T -ending codons determine the codon usage patterns in BRCA1 gene while more G/C-ending codons influence the codon usage pattern of AARS gene among mammals...
January 27, 2018: Genomics
N Galtier, C Roux, M Rousselle, J Romiguier, E Figuet, S Glémin, N Bierne, L Duret
Selection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. In animals, the population genetics of codon usage bias has only been studied in a handful of model organisms so far, and can be affected by confounding, non-adaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data we analysed the relationship between codon usage, gene expression, allele frequency distribution and recombination rate in 30 non-model species of animals, each from a different family, covering a wide range of effective population sizes...
January 30, 2018: Molecular Biology and Evolution
Sailen Barik
A significant number of proteins in all living species contains amino acid repeats (AARs) of various lengths and compositions, many of which play important roles in protein structure and function. Here, I have surveyed select homopolymeric single [(A)n] and double [(AB)n] AARs in the human proteome. A close examination of their codon pattern and analysis of RNA structure propensity led to the following set of empirical rules: (1) One class of amino acid repeats (Class I) uses a mixture of synonymous codons, some of which approximate the codon bias ratio in the overall human proteome; (2) The second class (Class II) disregards the codon bias ratio, and appears to have originated by simple repetition of the same codon (or just a few codons); and finally, (3) In all AARs (including Class I, Class II, and the in-betweens), the codons are chosen in a manner that precludes the formation of RNA secondary structure...
December 2017: Heliyon
Sophia S Liu, Adam J Hockenberry, Michael C Jewett, Luís A N Amaral
The unequal utilization of synonymous codons affects numerous cellular processes including translation rates, protein folding and mRNA degradation. In order to understand the biological impact of variable codon usage bias (CUB) between genes and genomes, it is crucial to be able to accurately measure CUB for a given sequence. A large number of metrics have been developed for this purpose, but there is currently no way of systematically testing the accuracy of individual metrics or knowing whether metrics provide consistent results...
January 2018: Journal of the Royal Society, Interface
Saurabh Mahajan, Deepa Agashe
Increasing growth rate across bacteria strengthens selection for faster translation, concomitantly increasing the total number of tRNA genes and codon usage bias (CUB: enrichment of specific synonymous codons in highly expressed genes). Typically, enriched codons are translated by tRNAs with higher gene copy numbers (GCN). A model of tRNA-CUB coevolution based on fast growth associated selection on translational speed recapitulates these patterns. A key untested implication of the coevolution model is that translational selection should favor higher tRNA GCN for more frequently used amino acids, potentially weakening the effect of growth associated selection on CUB...
January 29, 2018: Genome Biology and Evolution
Nicholas Di Paola, Caio César de Melo Freire, Paolo Marinho de Andrade Zanotto
Codon adaptation index (CAI) is a measure of synonymous codon usage biases given a usage reference. Through mutation, selection, and drift, viruses can optimize their replication efficiency and produce more offspring, which could increase the chance of secondary transmission. To evaluate how higher CAI towards the host has been associated with higher viral titers, we explored temporal trends of several historic and extensively sequenced zoonotic flaviviruses and relationships within the genus itself. To showcase evolutionary and epidemiological relationships associated with silent, adaptive synonymous changes of viruses, we used codon usage tables from human housekeeping and antiviral immune genes, as well as tables from arthropod vectors and vertebrate species involved in the flavivirus maintenance cycle...
2018: PloS One
Kathrin Eschke, Jakob Trimpert, Nikolaus Osterrieder, Dusan Kunec
Codon pair bias deoptimization (CPBD) has enabled highly efficient and rapid attenuation of RNA viruses. The technique relies on recoding of viral genes by increasing the number of codon pairs that are statistically underrepresented in protein coding genes of the viral host without changing the amino acid sequence of the encoded proteins. Utilization of naturally underrepresented codon pairs reduces protein production of recoded genes and directly causes virus attenuation. As a result, the mutant virus is antigenically identical with the parental virus, but virulence is reduced or absent...
January 29, 2018: PLoS Pathogens
Bryan S Kaplan, Carine K Souza, Phillip C Gauger, Charles B Stauft, J Robert Coleman, Steffen Mueller, Amy L Vincent
Influenza A virus (IAV) in swine constitutes a major economic burden for producers as well as a potential threat to public health. Whole inactivated virus vaccines (WIV) are the predominant countermeasure employed to control IAV in swine herds in the United States despite the superior protection, and diminished adverse effects, induced by live attenuated influenza vaccines (LAIV). A major hurdle for the development of LAIV exists in achieving the proper level of attenuation while maintaining immunogenicity...
January 20, 2018: Vaccine
Han Fang, Yi-Fei Huang, Aditya Radhakrishnan, Adam Siepel, Gholson J Lyon, Michael C Schatz
Ribosome profiling (Ribo-seq) is a powerful technique for measuring protein translation; however, sampling errors and biological biases are prevalent and poorly understood. Addressing these issues, we present Scikit-ribo (, an open-source analysis package for accurate genome-wide A-site prediction and translation efficiency (TE) estimation from Ribo-seq and RNA sequencing data. Scikit-ribo accurately identifies A-site locations and reproduces codon elongation rates using several digestion protocols (r = 0...
January 17, 2018: Cell Systems
Brett G Enos, Molly K Anthony, Joseph A DeGiorgis, Laura E Williams
Halobacteriovorax strains are saltwater-adapted predatory bacteria that attack Gram-negative bacteria and may play an important role in shaping microbial communities. To understand how Halobacteriovorax strains impact ecosystems and develop them as biocontrol agents, it is important to characterize variation in predation phenotypes and investigate Halobacteriovorax genome evolution. We isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island using Vibrio from the same site as prey. Small, fast-moving, attack-phase BE01 cells attach to and invade prey cells, consistent with the intraperiplasmic predation strategy of the H...
January 2018: MSphere
Bifang He, Katrina F Tjhung, Nicholas J Bennett, Ying Chou, Andrea Rau, Jian Huang, Ratmir Derda
Understanding the composition of a genetically-encoded (GE) library is instrumental to the success of ligand discovery. In this manuscript, we investigate the bias in GE-libraries of linear, macrocyclic and chemically post-translationally modified (cPTM) tetrapeptides displayed on the M13KE platform, which are produced via trinucleotide cassette synthesis (19 codons) and NNK-randomized codon. Differential enrichment of synthetic DNA {S}, ligated vector {L} (extension and ligation of synthetic DNA into the vector), naïve libraries {N} (transformation of the ligated vector into the bacteria followed by expression of the library for 4...
January 19, 2018: Scientific Reports
He Lu, Xin Qin, Jing Zhang, Shuang Zhang, Yu Zhu, Wei Hua Wu
Protozoan parasites can synthesize polyunsaturated fatty acids. They possess stearoyl-CoA desaturase to convert stearate into oleate and linoleate. Stearoyl-CoA desaturase are the key enzymes required for the synthesis of unsaturated fatty acids. It seems attractive to evaluate the possibility of using unsaturated fatty acid biosynthesis pathways as drug targets. In this study, the authors investigate codon usage bias, base composition variations and protein sequence in ten available complete stearoyl-CoA desaturase gene sequences from Toxoplasma gondii, Neospora caninum etc...
March 26, 2018: Acta Parasitologica
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