Codon optimization of nucleotide sequences is a widely used method to achieve high levels of transgene expression for basic and clinical research. Until now, immunological side effects have not been described. To trigger T cell responses against human papillomavirus, we incubated T cells with dendritic cells that were pulsed with RNA encoding the codon-optimized E7 oncogene. All T cell receptor...

Potency is a key optimization parameter for hemophilia A gene therapy product candidates. Optimization strategies include promoter engineering to increase transcription, codon optimization of mRNA to improve translation, and amino-acid substitution to promote secretion. Herein, we describe both rational and empirical design approaches to the development of a minimally sized, highly potent AAV-f...

In the problem of …nding an e¢ cient allocation when agents’utilities are privately known, we examine the e¤ect of restricting attention to mechanisms using “demand queries,” which ask agents to report an optimal allocation given a price list. We construct a combinatorial allocation problem with m items and two agents whose valuations lie in a certain class, such that (i) e¢ ciency can be obtai...

Background Microalgae are becoming a viable model for the expression of recombinant proteins. However, suitable levels of expression for commercial production have not yet been obtained. One way to increase the heterologous protein production is the codon optimization of the target gene so that it presents the preferential codons used by the host organism according to its own pool of transfer R...

Analysis of 〈X,R〉 models is considered as part of a general approach to solving optimization problems with fuzzy coefficients. This approach involves a modification of traditional optimization methods and is associated with formulating and solving one and the same problem within the framework of mutually interrelated models by constructing equivalent analogs with fuzzy coefficients in objective...

Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected if a need to match abundant tRNAs, and intermediacy of tRNA-mRNA interaction ...

We first review what is known about patterns of codon usage bias in Drosophila and make the following points: (i) Drosophila genes are as biased or more biased than those in microorganisms. (ii) The level of bias of genes and even the particular pattern of codon bias can remain phylogenetically invariant for very long periods of evolution. (iii) However, some genes, even very tightly linked gen...

Degeneracy in the genetic code implies that different codons can encode the same amino acid. Usage preference of synonymous codons has been observed in all domains of life. There is much evidence suggesting that this bias has a major role on protein elongation rate, contributing to differential expression and to co-translational folding. In addition to codon usage bias, other preference variati...

Standard vectors for high-level expression elicited undetectable levels of the gH and gL glycoproteins of rhesus monkey rhadinovirus (RRV) following transient-transfection assays under a variety of conditions. These same vectors and conditions yielded high levels of RRV gB expression. Unlike other genes of RRV, both the gH and gL genes were noted to have a highly aberrant, suboptimal codon usag...

BACKGROUND Variations in codon usage between species are one of the major causes affecting recombinant protein expression levels, with a significant impact on the economy of industrial enzyme production processes. The use of codon-optimized genes may overcome this problem. However, designing a gene for optimal expression requires choosing from a vast number of possible DNA sequences and differe...