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codon optimality

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https://www.readbyqxmd.com/read/28212334/transfer-of-anti-rotavirus-antibodies-during-pregnancy-and-in-milk-following-maternal-vaccination-with-a-herpes-simplex-virus-type-1-amplicon-vector
#1
Anita F Meier, Mark Suter, Elisabeth M Schraner, Bruno M Humbel, Kurt Tobler, Mathias Ackermann, Andrea S Laimbacher
Rotaviruses (RVs) are important enteric pathogens of newborn humans and animals, causing diarrhea and in rare cases death, especially in very young individuals. Rotavirus vaccines presently used are modified live vaccines that lack complete biological safety. Previous work from our laboratory suggested that vaccines based on in situ produced, non-infectious rotavirus-like particles (RVLPs) are efficient while being entirely safe. However, using either vaccine, active mucosal immunization cannot induce protective immunity in newborns due to their immature immune system...
February 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28209632/high-resolution-profiling-of-nmd-targets-in-yeast-reveals-translational-fidelity-as-a-basis-for-substrate-selection
#2
Alper Celik, Richard Baker, Feng He, Allan Jacobson
Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-Seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several non-coding RNAs...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28196196/identification-of-transthyretin-cardiac-amyloidosis-using-serum-retinol-binding-protein-4-and-a-clinical-prediction-model
#3
Marios Arvanitis, Clarissa M Koch, Gloria G Chan, Celia Torres-Arancivia, Michael P LaValley, Daniel R Jacobson, John L Berk, Lawreen H Connors, Frederick L Ruberg
Importance: Transthyretin cardiac amyloidosis (ATTR) is an underrecognized cause of heart failure (HF) in older individuals, owing in part to difficulty in diagnosis. ATTR can result from substitution of valine for isoleucine at codon 122 of the transthyretin (TTR) gene (V122I), present in 3.43% of African American individuals. Objective: To examine whether serum retinol-binding protein 4 (RBP4), an endogenous TTR ligand, could be used as a diagnostic test for ATTR V122I amyloidosis...
February 8, 2017: JAMA Cardiology
https://www.readbyqxmd.com/read/28187713/novel-methods-to-optimize-gene-and-statistic-test-for-evaluation-an-application-for-escherichia-coli
#4
Tran Tuan-Anh, Le Thi Ly, Ngo Quoc Viet, Pham The Bao
BACKGROUND: Since the recombinant protein was discovered, it has become more popular in many aspects of life science. The value of global pharmaceutical market was $87 billion in 2008 and the sales for industrial enzyme exceeded $4 billion in 2012. This is strong evidence showing the great potential of recombinant protein. However, native genes introduced into a host can cause incompatibility of codon usage bias, GC content, repeat region, Shine-Dalgarno sequence with host's expression system, so the yields can fall down significantly...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28182618/the-evolving-landscape-of-hiv-drug-resistance-diagnostics-for-expanding-testing-in-resource-limited-settings
#5
Seth C Inzaule, Raph L Hamers, Roger Paredes, Chunfu Yang, Rob Schuurman, Tobias F Rinke de Wit
Global scale-up of antiretroviral treatment (ART) has dramatically changed the prospects of HIV/AIDS disease rendering life-long chronic care and treatment a reality for millions of HIV-infected patients. Affordable technologies to monitor ART are needed to ensure long-term durability of limited available drug regimens. HIV drug resistance tests can complement existing strategies in optimizing clinical decision-making for patients with treatment failure, in addition to facilitating population-based surveillance of HIV drug resistance...
February 9, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28177830/analysis-of-codon-usage-patterns-in-morus-notabilis-based-on-genome-and-transcriptome-data
#6
Yan Wen, Ziliang Zou, Hongshun Li, Zhonghuai Xiang, Ningjia He
Codons play important roles in regulating gene expression levels and mRNA half-lives. However, codon usage and related studies in multicellular organisms still lag far behind those in unicellular organisms. In this study, we describe for the first time genome-wide patterns of codon bias in Morus notabilis (mulberry tree), and analyze genome-wide codon usage in 12 other Rosales species. The codon usage of M. notabilis was affected by nucleotide composition, mutation pressure, nature selection, and gene expression level...
January 3, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28167250/purification-and-characterization-of-human-dehydrodolychil-diphosphate-synthase-dhdds-overexpressed-in-e-coli
#7
Moshe Giladi, Ilan Edri, Michal Goldenberg, Hadas Newman, Roi Strulovich, Daniel Khananshvili, Yoni Haitin, Anat Loewenstein
Protein asparagine (N)-linked glycosylation is a post-translational modification that occurs in the endoplasmic reticulum; it plays an important role in protein folding, oligomerization, quality control, sorting, and transport. Accordingly, disorders of glycosylation may affect practically every organ system. Dehydrodolichyl diphosphate synthase (DHDDS) is an eukaryotic cis prenyltransferase (cis-PT) that catalyzes chain elongation of farnesyl diphosphate via multiple condensations with isopentenyl diphosphate to form dehydrodolichyl diphosphate, a precursor for the glycosyl carrier dolichylpyrophophate involved in N-linked glycosylation...
February 3, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28166648/characteristics-of-minimally-oversized-adeno-associated-virus-vectors-encoding-human-factor-viii-generated-using-producer-cell-lines-and-triple-transfection
#8
Bindu Nambiar, Cathleen Cornell Sookdeo, Patricia Berthelette, Robert Jackson, Susan Piraino, Brenda Burnham, Shelley Nass, David Souza, Catherine R O'Riordan, Karen A Vincent, Seng H Cheng, Donna Armentano, Sirkka Kyostio-Moore
Several ongoing clinical studies are evaluating recombinant adeno-associated virus (rAAV) vectors as gene delivery vehicles for a variety of diseases. However, the production of vectors with genomes >4.7 kb is challenging, with vector preparations frequently containing truncated genomes. To determine whether the generation of oversized rAAVs can be improved using a producer cell-line (PCL) process, HeLaS3-cell lines harboring either a 5.1 or 5.4 kb rAAV vector genome encoding codon-optimized cDNA for human B-domain deleted Factor VIII (FVIII) were isolated...
February 2017: Human Gene Therapy Methods
https://www.readbyqxmd.com/read/28166181/dna-vaccine-encoding-hpv16-oncogenes-e6-and-e7-induces-potent-cell-mediated-and-humoral-immunity-which-protects-in-tumor-challenge-and-drives-e7-expressing-skin-graft-rejection
#9
Janin Chandra, Julie L Dutton, Bo Li, Wai-Ping Woo, Yan Xu, Lynn K Tolley, Michelle Yong, James W Wells, Graham R Leggatt, Neil Finlayson, Ian H Frazer
We have previously shown that a novel DNA vaccine technology of codon optimization and the addition of ubiquitin sequences enhanced immunogenicity of a herpes simplex virus 2 polynucleotide vaccine in mice, and induced cell-mediated immunity when administered in humans at relatively low doses of naked DNA. We here show that a new polynucleotide vaccine using the same technology and encoding a fusion protein of the E6 and E7 oncogenes of high-risk human papillomavirus type 16 (HPV16) is immunogenic in mice. This vaccine induces long-lasting humoral and cell-mediated immunity and protects mice from establishment of HPV16-E7-expressing tumors...
February 2017: Journal of Immunotherapy
https://www.readbyqxmd.com/read/28163103/optimizing-antibody-expression-the-nuts-and-bolts
#10
REVIEW
B Vijayalakshmi Ayyar, Sushrut Arora, Shiva Shankar Ravi
Antibodies are extensively utilized entities in biomedical research, diagnostics, and therapeutics. Many of these applications require high amounts of antibodies. However, meeting this ever-increasing demand of antibodies in the global market is one of the outstanding challenges. The need to maintain a balance between demand and supply of antibodies has led the researchers to discover better means and methods for optimizing their expression. These strategies aim to increase the volumetric productivity of the antibodies along with the reduction of associated manufacturing costs...
February 2, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28163008/the-information-capacity-of-the-genetic-code-is-the-natural-code-optimal
#11
Ercan E Kuruoglu, Peter F Arndt
We envision the molecular evolution process as an information transfer process and provide a quantitative measure for information preservation in terms of the channel capacity according to the channel coding theorem of Shannon. We calculate Information capacities of DNA on the nucleotide (for non-coding DNA) and amino acid (for coding DNA) level using various substitution models. We extend our results on coding DNA to a discussion about the optimality of the natural codon-amino acid code. We provide the results of an adaptive search algorithm in the code domain and demonstrate the existence of a large number of genetic codes with higher information capacity...
February 2, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28157073/codon-optimization-underpins-generalist-parasitism-in-fungi
#12
Thomas Badet, Remi Peyraud, Malick Mbengue, Olivier Navaud, Mark Derbyshire, Richard P Oliver, Adelin Barbacci, Sylvain Raffaele
The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom...
February 3, 2017: ELife
https://www.readbyqxmd.com/read/28153045/visualizing-phylogenetic-tree-landscapes
#13
James C Wilgenbusch, Wen Huang, Kyle A Gallivan
BACKGROUND: Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems...
February 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28139884/streptomyces-venezuelae-tx-tl-a-next-generation-cell-free-synthetic-biology-tool
#14
Simon J Moore, Hung-En Lai, Hannah Needham, Karen M Polizzi, Paul S Freemont
Streptomyces venezuelae is a promising chassis in synthetic biology for fine chemical and secondary metabolite pathway engineering. The potential of S. venezuelae could be further realized by expanding its capability with the introduction of its own in vitro transcription-translation (TX-TL) system. TX-TL is a fast and expanding technology for bottom-up design of complex gene expression tools, biosensors and protein manufacturing. Herein, we introduce a S. venezuelae TX-TL platform by reporting a streamlined protocol for cell-extract preparation, demonstrating high-yield synthesis of a codon-optimized sfGFP reporter and the prototyping of a synthetic tetracycline-inducible promoter in S...
January 31, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28138738/expression-of-a-codon-optimized-%C3%AE-glucosidase-from-cellulomonas-flavigena-pr-22-in-saccharomyces-cerevisiae-for-bioethanol-production-from-cellobiose
#15
Francisco Javier Ríos-Fránquez, Enrique González-Bautista, Teresa Ponce-Noyola, Ana Carmela Ramos-Valdivia, Héctor Mario Poggi-Varaldo, Jaime García-Mena, Alfredo Martinez
Bioethanol is one of the main biofuels produced from the fermentation of saccharified agricultural waste; however, this technology needs to be optimized for profitability. Because the commonly used ethanologenic yeast strains are unable to assimilate cellobiose, several efforts have been made to express cellulose hydrolytic enzymes in these yeasts to produce ethanol from lignocellulose. The C. flavigenabglA gene encoding β-glucosidase catalytic subunit was optimized for preferential codon usage in S. cerevisiae...
January 30, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28134241/establishment-and-application-of-a-novel-isothermal-amplification-assay-for-rapid-detection-of-chloroquine-resistance-k76t-in-plasmodium-falciparum
#16
Madhvi Chahar, Neelima Mishra, Anup Anvikar, Rajnikant Dixit, Neena Valecha
Chloroquine (CQ) resistance in Plasmodium falciparum is determined by the mutations in the chloroquine resistance transporter (Pfcrt) gene. The point mutation at codon 76 (K76T), which has been observed in more than 91% of P. falciparum isolates in India, is the major determinant of CQ resistance. To overcome the limitations and challenges of traditional methods, in this investigation we developed an easy to use loop mediated isothermal amplification (LAMP) protocol for rapid detection of the K76T mutation associated with CQ resistance in P...
January 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28130769/secretory-expression-and-characterization-of-chinese-narcissus-gna-like-lectin-in-pichia-pastoris
#17
Xinyu Li, Pengpeng Zhang, Ning Zhang, Xiao Liang, Wenya Wang, Qipeng Yuan, Qiang Li
Narcissus tazetta lectin (NTL) is a GNA-like lectin, which has a wide potential application in medicine, agriculture, and glycobiology. In the present paper, the codon-optimized ntl gene was transformed into the yeast Pichia pastoris; SDS-PAGE gel and western blotting analysis revealed that the recombinant lectin was expressed successfully in Pichia yeast. The similarity between the recombinant NTL and the native NTL was confirmed by circular dichroism (CD) and hemagglutination assay further. In the 5-L scale fermentator, the protein yield was as high as 1...
January 27, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28129683/functional-and-key-gene-expression-analyses-of-chicken-monocyte-derived-dendritic-cells-with-recombinant-interleukin-4
#18
Hamideh Khajeh, Abbas Bahari, Milad Lagzian, Seyed Kazem Sabbagh
The central role of dendritic cells (DCs) as bridging innate and adaptive immunity leads to the expanding use of these cells in the poultry vaccine studies. The most effective way to produce enough DCs is monocyte transformation by combined induction of interleukin-4 (IL-4) and granulocyte-macrophage colony-stimulating factor (GM-CSF). In this study full length of chicken IL-4 (cIL-4) cDNA was cloned, characterized and expressed in Escherichia coli. Subsequently, the expressed IL-4 was used to induce monocytes- derived DCs (MDDC)...
December 2016: Iranian Journal of Allergy, Asthma, and Immunology
https://www.readbyqxmd.com/read/28122952/the-impact-of-selection-at-the-amino-acid-level-on-the-usage-of-synonymous-codons
#19
Paweł Błažej, Dorota Mackiewicz, Małgorzata Wnętrzak, Paweł Mackiewicz
There are two main forces that affect usage of synonymous codons: directional mutational pressure and selection. The effectiveness of protein translation is usually considered as the main selectional factor. However, the biased codon usage can be also a by-product of a general selection at the amino acid level interacting with nucleotide replacements. To evaluate the validity and strength of such effect, we superimposed more than 3.5 billion unrestricted mutational processes on the selection of non-synonymous substitutions based on the differences in physicochemical properties of the coded amino acids...
January 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28113866/codon-context-optimization-in-synthetic-gene-design
#20
Dimitris Papamichail, Hongmei Liu, Vitor Machado, Nathan Gould, J Robert Coleman, Georgios Papamichail
Advances in de novo synthesis of DNA and computational gene design methods make possible the customization of genes by direct manipulation of features such as codon bias and mRNA secondary structure. Codon context is another feature significantly affecting mRNA translational efficiency, but existing methods and tools for evaluating and designing novel optimized protein coding sequences utilize untested heuristics and do not provide quantifiable guarantees on design quality. In this study we examine statistical properties of codon context measures in an effort to better understand the phenomenon...
March 23, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
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