Read by QxMD icon Read

codon optimality

Michael Vogt, Christian Brüsseler, Jan van Ooyen, Michael Bott, Jan Marienhagen
The pentanol isomers 2-methyl-1-butanol and 3-methyl-1-butanol represent commercially interesting alcohols due to their potential application as biofuels. For a sustainable microbial production of these compounds, Corynebacterium glutamicum was engineered for producing 2-methyl-1-butanol and 3-methyl-1-butanol via the Ehrlich pathway from 2-keto-3-methylvalerate and 2-ketoisocaproate, respectively. In addition to an already available 2-ketoisocaproate producer, a 2-keto-3-methylvalerate accumulating C. glutamicum strain was also constructed...
October 13, 2016: Metabolic Engineering
D Evenson, P F Gerber, C T Xiao, P G Halbur, C Wang, D Tian, Y Y Ni, X J Meng, T Opriessnig
Current porcine reproductive and respiratory syndrome virus (PRRSV) vaccines sometimes fail to provide adequate immunity to protect pigs from PRRSV-induced disease. This may be due to antigenic differences among PRRSV strains. Rapid production of attenuated farm-specific homologous vaccines is a feasible alternative to commercial vaccines. In this study, attenuation and efficacy of a codon-pair de-optimized candidate vaccine generated by synthetic attenuated virus engineering approach (SAVE5) were tested in a conventional growing pig model...
October 11, 2016: Vaccine
Irene Zolotukhin, David M Markusic, Brett Palaschak, Brad E Hoffman, Meera A Srikanthan, Roland W Herzog
Hemophilia A and B are coagulation disorders resulting from the loss of functional coagulation factor VIII (FVIII) or factor IX proteins, respectively. Gene therapy for hemophilia with adeno-associated virus vectors has shown efficacy in hemophilia B patients. Although hemophilia A patients are more prevalent, the development of therapeutic adeno-associated virus vectors has been impeded by the size of the F8 cDNA and impaired secretion of FVIII protein. Further, it has been reported that over-expression of the FVIII protein induces endoplasmic reticulum stress and activates the unfolded protein response pathway both in vitro and in hepatocytes in vivo, presumably due to retention of misfolded FVIII protein within the endoplasmic reticulum...
2016: Molecular Therapy. Methods & Clinical Development
Dirk Landgraf, Dann Huh, Erinc Hallacli, Susan Lindquist
Gene tagging with fluorescent proteins is commonly applied to investigate the localization and dynamics of proteins in their cellular environment. Ideally, a fluorescent tag is genetically inserted at the endogenous locus at the N- or C- terminus of the gene of interest without disrupting regulatory sequences including the 5' and 3' untranslated region (UTR) and without introducing any extraneous unwanted "scar" sequences, which may create unpredictable transcriptional or translational effects. We present a reliable, low-cost, and highly efficient method for the construction of such scarless C-terminal and N-terminal fusions with fluorescent proteins in yeast...
2016: PloS One
Georg Wandrey, Joel Wurzel, Kyra Hoffmann, Tobias Ladner, Jochen Büchs, Lorenz Meinel, Tessa Lühmann
BACKGROUND: Genetic code expansion has developed into an elegant tool to incorporate unnatural amino acids (uAA) at predefined sites in the protein backbone in response to an amber codon. However, recombinant production and yield of uAA comprising proteins are challenged due to the additional translation machinery required for uAA incorporation. RESULTS: We developed a microtiter plate-based high-throughput monitoring system (HTMS) to study and optimize uAA integration in the model protein enhanced green fluorescence protein (eGFP)...
2016: Journal of Biological Engineering
Azeem Mehmood Butt, Izza Nasrullah, Raheel Qamar, Yigang Tong
The codon usage patterns of viruses reflect the evolutionary changes that allow them to optimize their survival and adapt their fitness to the external environment and, most importantly, their hosts. Here we report the genotype-specific codon usage patterns of Zika virus (ZIKV) strains from the current and previous outbreaks. Several genotype-specific and common codon usage traits were noted in the ZIKV coding sequences, indicating their independent evolutionary origins from a common ancestor. The overall influence of natural selection was more profound than that of mutation pressure, acting on a specific set of viral genes in the Asian-genotype ZIKV strains from the recent outbreak...
October 12, 2016: Emerging Microbes & Infections
Giuseppe Ronzitti, Giulia Bortolussi, Remco van Dijk, Fanny Collaud, Severine Charles, Christian Leborgne, Patrice Vidal, Samia Martin, Bernard Gjata, Marcelo Simon Sola, Laetitia van Wittenberghe, Alban Vignaud, Philippe Veron, Piter J Bosma, Andres F Muro, Federico Mingozzi
Crigler-Najjar syndrome is a severe metabolic disease of the liver due to a reduced activity of the UDP Glucuronosyltransferase 1A1 (UGT1A1) enzyme. In an effort to translate to the clinic an adeno-associated virus vector mediated liver gene transfer approach to treat Crigler-Najjar syndrome, we developed and optimized a vector expressing the UGT1A1 transgene. For this purpose, we designed and tested in vitro and in vivo multiple codon-optimized UGT1A1 transgene cDNAs. We also optimized noncoding sequences in the transgene expression cassette...
2016: Molecular Therapy. Methods & Clinical Development
Md Nasimuzzaman, Danielle Lynn, Rebecca Ernst, Michele Beuerlein, Richard H Smith, Archana Shrestha, Scott Cross, Kevin Link, Carolyn Lutzko, Diana Nordling, David W Russell, Andre Larochelle, Punam Malik, Johannes C M Van der Loo
Compared to other integrating viral vectors, foamy virus (FV) vectors have distinct advantages as a gene transfer tool, including their nonpathogenicity, the ability to carry larger transgene cassettes, and increased stability of virus particles due to DNA genome formation within the virions. Proof of principle of its therapeutic utility was provided with the correction of canine leukocyte adhesion deficiency using autologous CD34(+) cells transduced with FV vector carrying the canine CD18 gene, demonstrating its long-term safety and efficacy...
2016: Molecular Therapy. Methods & Clinical Development
Jae Ho Shin, Seok Hyun Park, Young Hoon Oh, Jae Woong Choi, Moon Hee Lee, Jae Sung Cho, Ki Jun Jeong, Jeong Chan Joo, James Yu, Si Jae Park, Sang Yup Lee
BACKGROUND: 5-Aminovaleric acid (5AVA) is an important five-carbon platform chemical that can be used for the synthesis of polymers and other chemicals of industrial interest. Enzymatic conversion of L-lysine to 5AVA has been achieved by employing lysine 2-monooxygenase encoded by the davB gene and 5-aminovaleramidase encoded by the davA gene. Additionally, a recombinant Escherichia coli strain expressing the davB and davA genes has been developed for bioconversion of L-lysine to 5AVA...
October 7, 2016: Microbial Cell Factories
Anay Kumar Maurya, Deepak Parashar, T Satyanarayana
Thermophilc mold Sporotrichum thermophile secretes an acidstable and thermostable phytase, which finds application as a food and feed additive because of its adequate thermostability, acid stability, protease insensitivity and broad substrate spectrum. Low extracellular phytase production by the mold is a major bottleneck for its application on a commercial scale. We have successfully overcome this problem by constitutive secretary expression of codon optimized rStPhy under glyceraldehyde phosphate dehydrogenase (GAP) promoter in Pichia pastoris...
September 30, 2016: International Journal of Biological Macromolecules
Wei Jiang, Beibei Lv, Xiao Wu, Jinbin Wang, Guogan Wu, Chunhui Shi, Xueming Tang
In this study, trends in synonymous codons usage of V. volvecea have been firstly examined by analysis of complete coding sequences and gene-chip data. The results showed that GC content at three codon positions are obviously different and there were several factors shaping the codon usage of V. volvacea genes, including base composition. The comparison of codon usage among four edible fungi such as V. volvacea, Agaricus bisporus, Coprinopsis cinerea and Pleurotus ostreatus indicated that similarly codon usage pattern was used among V...
October 3, 2016: Biotechnology and Applied Biochemistry
Bianca S Siedler, Bárbara C Roloff, Gizele L de Sá, Alessandra Neis, Fabrício R Conceição, Daiane D Hartwig, Sibele Borsuk, Odir A Dellagostin, Fabrício S Campos, Paulo M Roehe, Claudia P Hartleben, Alan J A McBride
Bovine herpesvirus (BoHV) glycoprotein E (gE) is a non-essential envelope glycoprotein and the deletion of gE has been used to develop BoHV-1 and BoHV-5 differential vaccine strains. The DIVA (Differentiation of Infected from Vaccinated Animals) strategy, using marker vaccines based on gE-negative BoHV strains, allows the identification of vaccinated or infected animals in immunoassays designed to detect anti-gE antibodies. In this study a codon optimized synthetic sequence of gE containing highly conserved regions from BoHV-1 and BoHV-5 was expressed in Pichia pastoris...
September 28, 2016: Protein Expression and Purification
Sudeesh Karumathil, Vijaya R Dirisala, Uthpala Srinadh, Valaboju Nikhil, N Satya Sampath Kumar, Rahul R Nair
Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed...
2016: Bioinformatics and Biology Insights
Magdalena Bodnar, Paweł Burduk, Paulina Antosik, Małgorzata Jarmuz-Szymczak, Malgorzata Wierzbicka, Andrzej Marszalek
BACKGROUND: The role of BRAF mutations in cancerogenesis has been demonstrated in several solid tumor types. However, in salivary gland tumors, this genetic alteration is very uncommon, and its role still remains unclear. Thus, the aim of this study was to analyze BRAF V600E (VE1) protein expression with BRAF mutation status in codon 600, in malignant and benign salivary gland tumors. METHODS: Studies were performed on archived formalin-fixed paraffin-embedded tissue sections derived from 95 patients who underwent surgery for tumors of the salivary gland...
September 28, 2016: Journal of Oral Pathology & Medicine
Eytan Zlotorynski
No abstract text is available yet for this article.
September 28, 2016: Nature Reviews. Molecular Cell Biology
Kai Yu, Kok Siong Ang, Dong-Yup Lee
Codon optimization has been widely used for designing native or synthetic genes to enhance their expression in heterologous host organisms. We recently developed Codon Optimization On-Line (COOL) which is a web-based tool to provide multi-objective codon optimization functionality for synthetic gene design. COOL provides a simple and flexible interface for customizing codon optimization based on several design parameters such as individual codon usage, codon pairing, and codon adaptation index. User-defined sequences can also be compared against the COOL optimized ones to show the extent by which the user's sequences can be evaluated and further improved...
2017: Methods in Molecular Biology
Zhipeng Zhou, Yunkun Dang, Mian Zhou, Lin Li, Chien-Hung Yu, Jingjing Fu, She Chen, Yi Liu
Codon usage biases are found in all eukaryotic and prokaryotic genomes, and preferred codons are more frequently used in highly expressed genes. The effects of codon usage on gene expression were previously thought to be mainly mediated by its impacts on translation. Here, we show that codon usage strongly correlates with both protein and mRNA levels genome-wide in the filamentous fungus Neurospora Gene codon optimization also results in strong up-regulation of protein and RNA levels, suggesting that codon usage is an important determinant of gene expression...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Vishwa Jyoti Baruah, Siddhartha Sankar Satapathy, Bhesh Raj Powdel, Rocktotpal Konwarh, Alak Kumar Buragohain, Suvendra Kumar Ray
The present study was undertaken to investigate the pattern of optimal codon usage in Archaea. Comparative analysis was executed to understand the pattern of codon usage bias between the high expression genes (HEG) and the whole genomes in two Archaeal phyla, Crenarchaea and Euryarchaea. The G+C% of the HEG was found to be less in comparison to the genome G+C% in Crenarchaea, whereas reverse was the case in Euryarchaea. The preponderance of U/A ending codons that code for HEG in Crenarchaea was in sharp contrast to the C/G ended ones in Euryarchaea...
September 2016: Journal of Genetics
Nicole Armbruster, Annalisa Lattanzi, Matthieu Jeavons, Laetitia Van Wittenberghe, Bernard Gjata, Thibaut Marais, Samia Martin, Alban Vignaud, Thomas Voit, Fulvio Mavilio, Martine Barkats, Ana Buj-Bello
Spinal muscular atrophy (SMA) is an autosomal recessive disease of variable severity caused by mutations in the SMN1 gene. Deficiency of the ubiquitous SMN function results in spinal cord α-motor neuron degeneration and proximal muscle weakness. Gene replacement therapy with recombinant adeno-associated viral (AAV) vectors showed therapeutic efficacy in several animal models of SMA. Here, we report a study aimed at analyzing the efficacy and biodistribution of a serotype-9, self-complementary AAV vector expressing a codon-optimized human SMN1 coding sequence (coSMN1) under the control of the constitutive phosphoglycerate kinase (PGK) promoter in neonatal SMNΔ7 mice, a severe animal model of the disease...
2016: Molecular Therapy. Methods & Clinical Development
Jerome Ambroise, Jamal Badir, Louise Nienhaus, Annie Robert, Anne-France Dekairelle, Jean-Luc Gala
BACKGROUND: Pyrosequencing Allele Quantification (AQ) is a cost-effective DNA sequencing method that can be used for detecting somatic mutations in formalin-fixed paraffin-embedded (FFPE) samples. The method displays a low turnaround time and a high sensitivity. Pyrosequencing suffers however from two main drawbacks including (i) low specificity and (ii) difficult signal interpretation when multiple mutations are reported in a hotspot genomic region. RESULTS: Using a constraint-based regression method, the new AdvISER-PYRO-SMQ algorithm was developed in the current study and implemented into an R package...
2016: Algorithms for Molecular Biology: AMB
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"