keyword
MENU ▼
Read by QxMD icon Read
search

codon optimality

keyword
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
#1
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/28448543/heterologous-expression-of-a-thermophilic-diacylglycerol-acyltransferase-triggers-triglyceride-accumulation-in-escherichia-coli
#2
Beatriz Lázaro, Juan A Villa, Omar Santín, Matilde Cabezas, Cintia D F Milagre, Fernando de la Cruz, Gabriel Moncalián
Triglycerides (TAGs), the major storage molecules of metabolic energy and source of fatty acids, are produced as single cell oil by some oleogenic microorganisms. However, these microorganisms require strict culture conditions, show low carbon source flexibilities, lack efficient genetic modification tools and in some cases pose safety concerns. TAGs have essential applications such as behaving as a source for added-value fatty acids or giving rise to the production of biodiesel. Hence, new alternative methods are urgently required for obtaining these oils...
2017: PloS One
https://www.readbyqxmd.com/read/28447574/optimized-longitudinal-monitoring-of-stem-cell-grafts-in-mouse-brain-using-a-novel-bioluminescent-near-infrared-fluorescent-fusion-reporter
#3
Laura Mezzanotte, Juvita Delancy Iljas, Ivo Que, Alan Chan, Eric Kaijzel, Rob Hoeben, Clemens Löwik
<p>Biodistribution and fate of transplanted stem cells via longitudinal monitoring has been successfully achievedin the last decade using optical imaging. However, sensitive longitudinal imaging of transplanted stem cells in deep tissue like the brain remains challenging not only due to low light penetration but because of other factors such as low or inferior expression levels of optical reporters in stem cells and stem cell death after transplantation. Here we describe an optimized imaging protocol for sensitive long term monitoring of human bone marrow derived mesenchymal stem cells (hMSCs) expressing a novel bioluminescent/near infrared fluorescent (NIRF) fusion reporter transplanted in mouse brain cortex...
April 26, 2017: Cell Transplantation
https://www.readbyqxmd.com/read/28442431/reducing-isoform-complexity-of-human-tetraspanins-by-optimized-expression-in-dictyostelium-discoideum-enables-high-throughput-functional-read-out
#4
Tineke Scheltz, Julia von Bülow, Eric Beitz
The human tetraspanin family of scaffold proteins comprises 33 isoforms. Being integral membrane proteins, they organize a so-called tetraspanin web via homomeric and heteromeric protein-protein interactions with integrins, immunoglobulins, growth factors, receptor tyrosine kinases, proteases, signaling proteins, and viral capsid proteins. Tetraspanins promote cellular effects, such as adhesion, migration, invasion, signaling, membrane fusion, protein trafficking, cancer progression, and infections. The ubiquitous expression of multiple tetraspanin isoforms and partner proteins hampers specific interaction studies...
April 22, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28441787/codon-usage-optimization-and-construction-of-plasmid-encoding-iranian-human-papillomavirus-type-16-e7-oncogene-for-lactococcus-lactis-subsp-cremoris-mg1363
#5
Amir Hossein Mohseni, Vadood Razavilar, Hossein Keyvani, Mohammad Reza Razavi, Ramazan Ali Khavari Nejad
HPV 16 intratypic sequence variations has been recognized in association with oncogenic potential diverge and geographic distribution. This study aimed to investigate nucleotide modifications and optimization of HPV 16 E7 regions from Iranian infected women. Cervical biopsies from 79/163 HPV 16 positive cancer patients detected in our study were analyzed by PCR in a couple of cloning of a complete ORF of the E7 gene, and sequencing. The most frequently observed variant was C196T in E7 which led to an amino acid change of R66W...
March 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28435908/development-of-a-japanese-encephalitis-virus-like-particle-vaccine-in-silkworms-using-codon-optimised-prm-and-envelope-genes
#6
Sayaka Matsuda, Reiko Nerome, Kenichi Maegawa, Akira Kotaki, Shigeo Sugita, Kazunori Kawasaki, Kazumichi Kuroda, Ryoji Yamaguchi, Tomohiko Takasaki, Kuniaki Nerome
We have successfully prepared a Japanese encephalitis virus (JEV) - Nakayama virus like particle (NVLP) vaccine using synthetic codon-optimized prM and E genes. The expression of the recombinant JEV Nakayama-BmNPV (JEV-NNPV) virus was determined in infected silkworm Bm-N cells by fluorescence and Western blot analysis. The recombinant was inoculated into silkworm pupae and the yield of Nakayama VLP (NVLP) reached a peak in the homogenates after 3 days. Additionally, in the peptide analysis of infected pupae homogenate, it appeared approximately 300-500 μg E protein/pupa were produced...
April 2017: Heliyon
https://www.readbyqxmd.com/read/28431990/a-common-polymorphism-decreases-lrp1-mrna-stability-and-is-associated-with-increased-plasma-factor-viii-levels
#7
Jiann-Der Lee, Kuang-Ming Hsiao, Pey-Jium Chang, Chih-Cheng Chen, Ya-Wen Kuo, Yen-Chu Huang, Huan-Lin Hsu, Ya-Hui Lin, Chih-Ying Wu, Ying-Chih Huang, Meng Lee, Chia-Yu Hsu, Yi-Ting Pan, Chih-Yu Kuo, Chun-Hsien Lin
The low-density lipoprotein receptor-related protein 1 (LRP1) gene is associated with increased levels of plasma factor VIII (FVIII). We aimed to explore eight functional genetic LRP1 variants for their potential roles in regulating FVIII levels and acute ischemic stroke (AIS). This genetic association study enrolled 192 patients with AIS and 134 controls. There were no significant differences in the genetic frequency of the eight functional single-nucleotide polymorphisms (SNPs) between the control and AIS groups...
April 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28428795/non-canonical-translation-in-plant-rna-viruses
#8
REVIEW
Manuel Miras, W Allen Miller, Verónica Truniger, Miguel A Aranda
Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5' cap structure and/or the 3' poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28427327/analysis-of-transcriptome-data-reveals-multifactor-constraint-on-codon-usage-in-taenia-multiceps
#9
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/28419821/expression-of-the-enzymatically-active-legumain-like-cysteine-proteinase-tvlegu-1-of-trichomonas-vaginalis-in-pichia-pastoris
#10
Gerardo Reséndiz-Cardiel, Rossana Arroyo, Jaime Ortega-López
The legumain-like cysteine proteinase TvLEGU-1 from Trichomonas vaginalis plays a major role in trichomonal cytoadherence. However, its structure-function characterization has been limited by the lack of a reliable recombinant expression platform to produce this protein in its native folded conformation. TvLEGU-1 has been expressed in Escherichia coli as inclusion bodies and all efforts to refold it have failed. Here, we describe the expression of the synthetic codon-optimized tvlegu-1 (tvlegu-1-opt) gene in Pichia pastoris strain X-33 (Mut+) under the inducible AOX1 promoter...
April 15, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28418615/co-expression-of-gr79-epsps-and-gat-yields-herbicide-resistant-cotton-with-low-glyphosate-residues
#11
Chengzhen Liang, Bao Sun, Zhigang Meng, Zhaohong Meng, Yuan Wang, Guoqing Sun, Tao Zhu, Wei Lu, Wei Zhang, Waqas Malik, Min Lin, Rui Zhang, Sandui Guo
Glyphosate resistant (GR) crops have been adopted on a massive scale by North and South American farmers. Currently, about 80% of the 120 million hectares of the global genetically-modified (GM) crops are GR crop varieties. However, the adoption of GR plants in China has not occurred at the same pace, owing to several factors including, among other things, labor markets and the residual effects of glyphosate in transgenic plants. Here, we report the co-expression of codon-optimized forms of GR79 EPSPS and N-acetyltransferase (GAT) genes in cotton...
April 18, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28418108/metabolic-characterization-and-transformation-of-the-non-dairy-lactococcus-lactis-strain-kf147-for-production-of-ethanol-from-xylose
#12
Kia Vest Petersen, Jianming Liu, Jun Chen, Jan Martinussen, Peter Ruhdal Jensen, Christian Solem
The non-dairy lactic acid bacterium Lactococcus lactis KF147 can utilize xylose as the sole energy source. To assess whether KF147 could serve as a platform organism for converting second generation sugars into useful chemicals, we characterized growth and product formation for KF147 when grown on xylose. In a defined medium KF147 was found to co-metabolize xylose and arginine, resulting in bi-phasic growth. Especially at low xylose concentrations, arginine significantly improved growth rate. To facilitate further studies of the xylose metabolism, we eliminated arginine catabolism by deleting the arcA gene encoding the arginine deiminase...
April 18, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28411891/recombinant-expression-of-thermobifida-fusca-e7-lpmo-in-pichia-pastoris-and-escherichia-coli-and-their-functional-characterization
#13
Kelly B Rodrigues, Jéssica K A Macêdo, Tallyta Teixeira, Jéssica S Barros, Ana C B Araújo, Fernanda P Santos, Betânia F Quirino, Bruno S A F Brasil, Thaís F C Salum, Patrícia V Abdelnur, Léia C L Fávaro
The discovery of lytic polysaccharides monooxygenases copper dependent (LPMOs) revolutionized the classical concept that the cleavage of cellulose is a hydrolytic process in recent years. These enzymes carry out oxidative cleavage of cellulose (and other polysaccharides), acting synergistically with cellulases and other hydrolases. In fact, LPMOs have the potential for increasing the efficiency of the lignocellulosic biomass conversion in biofuels and high value chemicals. Among a small number of microbial LPMOs that have been characterized, some LPMOs were expressed and characterized biochemically from the bacteria Thermobifida fusca, using the host Escherichia coli...
April 9, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/28408474/when-mrna-translation-meets-decay
#14
REVIEW
Alicia A Bicknell, Emiliano P Ricci
Messenger RNA (mRNA) translation and mRNA degradation are important determinants of protein output, and they are interconnected. Previously, it was thought that translation of an mRNA, as a rule, prevents its degradation. mRNA surveillance mechanisms, which degrade mRNAs as a consequence of their translation, were considered to be exceptions to this rule. Recently, however, it has become clear that many mRNAs are degraded co-translationally, and it has emerged that codon choice, by influencing the rate of ribosome elongation, affects the rate of mRNA decay...
April 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28405630/efficient-and-robust-paramyxoviridae-reverse-genetics-systems
#15
Shannon M Beaty, Arnold Park, Sohui T Won, Patrick Hong, Michael Lyons, Frederic Vigant, Alexander N Freiberg, Benjamin R tenOever, W Paul Duprex, Benhur Lee
The notoriously low efficiency of Paramyxoviridae reverse genetics systems has posed a limiting barrier to the study of viruses in this family. Previous approaches to reverse genetics have utilized a wide variety of techniques to overcome the technical hurdles. Although robustness (i.e., the number of attempts that result in successful rescue) has been improved in some systems with the use of stable cell lines, the efficiency of rescue (i.e., the proportion of transfected cells that yield at least one successful rescue event) has remained low...
March 2017: MSphere
https://www.readbyqxmd.com/read/28390761/the-aav-mediated-and-rna-guided-crispr-cas9-system-for-gene-therapy-of-dmd-and-bmd
#16
REVIEW
Jing-Zhang Wang, Peng Wu, Zhi-Min Shi, Yan-Li Xu, Zhi-Jun Liu
Mutations in the dystrophin gene (Dmd) result in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD), which afflict many newborn boys. In 2016, Brain and Development published several interesting articles on DMD treatment with antisense oligonucleotide, kinase inhibitor, and prednisolone. Even more strikingly, three articles in the issue 6271 of Science in 2016 provide new insights into gene therapy of DMD and BMD via the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)...
April 5, 2017: Brain & Development
https://www.readbyqxmd.com/read/28389350/process-development-for-production-and-purification-of-the-schistosoma-mansoni-sm14-antigen
#17
Leonardo Damasceno, Gerd Ritter, Carl A Batt
The trematode Schistosoma mansoni Sm14 antigen was expressed in the yeast Pichia pastoris and secreted into the culture medium at yields of approximately 250 mg L(-1). Sm14 belongs to a family of fatty-acid binding proteins and appears to play an important role in uptake, transport, and compartmentalization of lipids in S. mansoni and it is a potential vaccine candidate in both humans and domesticated animals. The Sm14 gene was codon-optimized for expression in P. pastoris, and placed under transcription of the strong methanol inducible AOX1 promoter...
April 5, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28388355/in-silico-analysis-of-l1-l2-sequences-of-human-papillomaviruses-implication-for-universal-vaccine-design
#18
Nazila Ghorban Hosseini, Majid Tebianian, Ayoub Farhadi, Ali Hossein Khani, Arian Rahimi, Mojtaba Mortazavi, Seyed Younes Hosseini, Morteza Taghizadeh, Mahsa Rezaei, Mehdi Mahdavi
The aim of this study was to design a multiepitope universal vaccine for major human papillomavirus (HPV) structural proteins, L1/L2, by bioinformatics models. For this purpose, we predicted the most probable immunogenic epitopes of L1 and L2 from common high-risk HPV 16, 18, 31, and 45 beside high prevalent type 6 and 11 based on BCPREDS defaulted model, while solvent accessibility of structure was extrapolated. The three-dimensional molecular model of L1 protein was constructed by Swiss Model server, whereas sequence alignment provided model for prediction of L2 protein epitopes...
April 2017: Viral Immunology
https://www.readbyqxmd.com/read/28376863/pichia-pastoris-versus-saccharomyces-cerevisiae-a-case-study-on-the-recombinant-production-of-human-granulocyte-macrophage-colony-stimulating-factor
#19
Anh-Minh Tran, Thanh-Thao Nguyen, Cong-Thuan Nguyen, Xuan-Mai Huynh-Thi, Cao-Tri Nguyen, Minh-Thuong Trinh, Linh-Thuoc Tran, Stephanie P Cartwright, Roslyn M Bill, Hieu Tran-Van
BACKGROUND: Recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) is a glycoprotein that has been approved by the FDA for the treatment of neutropenia and leukemia in combination with chemotherapies. Recombinant hGM-CSF is produced industrially using the baker's yeast, Saccharomyces cerevisiae, by large-scale fermentation. The methylotrophic yeast, Pichia pastoris, has emerged as an alternative host cell system due to its shorter and less immunogenic glycosylation pattern together with higher cell density growth and higher secreted protein yield than S...
April 4, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28374071/biosynthesis-of-di-rhamnolipids-and-variations-of-congeners-composition-in-genetically-engineered-escherichia-coli
#20
Jin Du, Aijun Zhang, Jian'an Hao, Jing Wang
OBJECTIVES: To engineer Escherichia coli for the heterologous production of di-rhamnolipids, which are important biosurfactants but mainly produced by opportunistic pathogen Pseudomonas aeruginosa. RESULTS: The codon-optimized rhlAB and rhlC genes originating from P. aeruginosa and Burkholderia pseudomallei were combinatorially expressed in E. coli to produce di-rhamnolipids with varied congeners compositions. Genes involved in endogenous upstream pathways (rhamnose and fatty acids synthesis) were co-overexpressed with rhlAB-rhlC, resulting in variations of rhamnolipids production and congeners compositions...
April 3, 2017: Biotechnology Letters
keyword
keyword
52405
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"