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https://www.readbyqxmd.com/read/28932252/transient-expression-of-lumbrokinase-pi239-in-tobacco-nicotiana-tabacum-using-a-geminivirus-based-single-replicon-system-dissolves-fibrin-and-blood-clots
#1
Alexia Dickey, Nan Wang, Edwin Cooper, Lauren Tull, Drew Breedlove, Hugh Mason, Dehu Liu, Kevin Yueju Wang
Lumbrokinases, a group of fibrinolytic enzymes extracted from earthworm, have been widely used to prevent and treat various cardiovascular diseases. They specifically target fibrin to effectively degrade thrombi without major side effects. Plant expression systems are becoming potential alternative expression platforms for producing pharmaceutical proteins. In this work, a lumbrokinase (PI239) was produced from a plant system. Both wild-type (WT) and plant codon-optimized (OP) PI239 gene sequences were synthesized and cloned into a geminivirus-based single-vector DNA replicon system...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/28929019/heterologous-expression-of-plasmodium-vivax-apical-membrane-antigen-1-pvama1-for-binding-peptide-selection
#2
Ching Hoong Chew, Yvonne Ai Lian Lim, Kek Heng Chua
BACKGROUND: Plasmodium is an obligate intracellular parasite. Apical membrane antigen 1 (AMA1) is the most prominent and well characterized malarial surface antigen that is essential for parasite-host cell invasion, i.e., for sporozoite to invade and replicate within hepatocytes in the liver stage and merozoite to penetrate and replicate within erythrocytes in the blood stage. AMA1 has long served as a potent antimalarial drug target and is a pivotal vaccine candidate. A good understanding of the structure and molecular function of this Plasmodium protein, particularly its involvement in host-cell adhesion and invasion, is of great interest and hence it offers an attractive target for the development of novel therapeutics...
2017: PeerJ
https://www.readbyqxmd.com/read/28927382/a-rapid-seamless-method-for-gene-knockout-in-pseudomonas-aeruginosa
#3
Weiliang Huang, Angela Wilks
BACKGROUND: Pseudomonas aeruginosa is a model organism for the study of quorum sensing, biofilm formation, and also leading cause of nosocomial infections in immune compromised patients. As such P. aeruginosa is one of the most well studied organisms in terms of its genetics. However, the construction of gene deletions and replacements in Pseudomonas aeruginosa is relatively time-consuming, requiring multiple steps including suicide vector construction, conjugation, inactivation with insertion of antibiotic resistance cassettes and allelic exchange...
September 19, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28924459/genetic-code-optimization-for-cotranslational-protein-folding-codon-directional-asymmetry-correlates-with-antiparallel-betasheets-trna-synthetase-classes
#4
Hervé Seligmann, Ganesh Warthi
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28921302/comparative-evolutionary-genomics-of-corynebacterium-with-special-reference-to-codon-and-amino-acid-usage-diversities
#5
Shilpee Pal, Indrani Sarkar, Ayan Roy, Pradeep K Das Mohapatra, Keshab C Mondal, Arnab Sen
The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium...
September 18, 2017: Genetica
https://www.readbyqxmd.com/read/28920716/transposons-moving-forward-from-preclinical-studies-to-clinical-trials
#6
Jaitip Tipanee, Thierry VandenDriessche, Marinee K Chuah
Transposons have emerged as promising vectors for gene therapy that can potentially overcome some of the limitations of commonly used viral vectors. Transposons stably integrate into the target cell genome, enabling persistent expression of therapeutic genes. Transposons have evolved from being used as basic tools in biomedical research to bona fide therapeutics. Currently, the most promising transposons for gene therapy applications are derived from Sleeping Beauty (SB) or piggyBac (PB). Stable transposition requires co-delivery of the transposon DNA with the corresponding transposase gene, mRNA, or protein...
August 22, 2017: Human Gene Therapy
https://www.readbyqxmd.com/read/28919581/antitumor-response-to-a-codon-optimized-hpv-16-e7-hsp70-fusion-antigen-dna-vaccine
#7
Hoorieh Soleimanjahi, Hadi Razavinikoo, Fatemeh Fotouhi, Abdollah Ardebili
BACKGROUND: Vaccines based on virus-like particles are effective against Human Papilloma Virus (HPV) infection; however, they have not shown a therapeutic effect against HPV-associated diseases. New immunotherapy strategies based on immune responses against tumor antigens can positively affect the clearance of HPV-associated lesions. OBJECTIVE: To generate two therapeutic fusion DNA vaccines (optimizedE7/mouseHSP70 and wildE7/mouseHSP70) to induce antitumor specific responses in mice models...
September 2017: Iranian Journal of Immunology: IJI
https://www.readbyqxmd.com/read/28918040/codon-optimized-p1a-encoding-dna-vaccine-toward-a-therapeutic-vaccination-against-p815-mastocytoma
#8
Alessandra Lopes, Kevin Vanvarenberg, Véronique Préat, Gaëlle Vandermeulen
DNA vaccine can be modified to increase protein production and modulate immune response. To enhance the efficiency of a P815 mastocytoma DNA vaccine, the P1A gene sequence was optimized by substituting specific codons with synonymous ones while modulating the number of CpG motifs. The P815A murine antigen production was increased with codon-optimized plasmids. The number of CpG motifs within the P1A gene sequence modulated the immunogenicity by inducing a local increase in the cytokines involved in innate immunity...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28917035/selgenamic-an-algorithm-for-selenoprotein-gene-assembly
#9
Liang Jiang, Qiong Liu
Computational methods for identifying selenoproteins have been developed rapidly in recent years. However, it is still difficult to identify the open reading frame (ORF) of eukaryotic selenoprotein gene, because the TGA codon for a selenocysteine (Sec) residue in the active center of selenoprotein is traditionally a terminal signal of protein translation. A gene assembly algorithm SelGenAmic has been constructed and presented in this chapter for identifying selenoprotein genes from eukaryotic genomes. A method based on this algorithm was developed to build an optimal TGA-containing-ORF for each TGA in a genome, followed by protein similarity analysis through conserved sequence alignments to screen out selenoprotein genes from these ORFs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28905885/long-term-correction-of-hemophilia-a-mice-following-lentiviral-mediated-delivery-of-an-optimized-canine-factor-viii-gene
#10
J M Staber, M J Pollpeter, C-G Anderson, M Burrascano, A L Cooney, P L Sinn, D T Rutkowski, W C Raschke, P B McCray
Current therapies for hemophilia A include frequent prophylactic or on-demand intravenous factor treatments which are costly, inconvenient and may lead to inhibitor formation. Viral vector delivery of factor VIII (FVIII) cDNA has the potential to alleviate the debilitating clotting defects. Lentiviral-based vectors delivered to murine models of hemophilia A mediate phenotypic correction. However, a limitation of lentiviral-mediated FVIII delivery is inefficient transduction of target cells. Here, we engineer a feline immunodeficiency virus (FIV) -based lentiviral vector pseudotyped with the baculovirus GP64 envelope glycoprotein to mediate efficient gene transfer to mouse hepatocytes...
September 14, 2017: Gene Therapy
https://www.readbyqxmd.com/read/28904370/in-planta-expression-of-hyperthermophilic-enzymes-as-a-strategy-for-accelerated-lignocellulosic-digestion
#11
Bilal Ahmad Mir, Alexander A Myburg, Eshchar Mizrachi, Don A Cowan
Conversion of lignocellulosic biomass to biofuels and biomaterials suffers from high production costs associated with biomass pretreatment and enzymatic hydrolysis. In-planta expression of lignocellulose-digesting enzymes is a promising approach to reduce these cost elements. However, this approach faces a number of challenges, including auto-hydrolysis of developing cell walls, plant growth and yield penalties, low expression levels and the limited stability of expressed enzymes at the high temperatures generally used for biomass processing to release fermentable sugars...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28902855/improving-heterologous-membrane-protein-production-in-escherichia-coli-by-combining-transcriptional-tuning-and-codon-usage-algorithms
#12
Nico J Claassens, Melvin F Siliakus, Sebastiaan K Spaans, Sjoerd C A Creutzburg, Bart Nijsse, Peter J Schaap, Tessa E F Quax, John van der Oost
High-level, recombinant production of membrane-integrated proteins in Escherichia coli is extremely relevant for many purposes, but has also been proven challenging. Here we study a combination of transcriptional fine-tuning in E. coli LEMO21(DE3) with different codon usage algorithms for heterologous production of membrane proteins. The overexpression of 6 different membrane proteins is compared for the wild-type gene codon usage variant, a commercially codon-optimized variant, and a codon-harmonized variant...
2017: PloS One
https://www.readbyqxmd.com/read/28901843/coevolution-of-the-translational-machinery-optimizes-initiation-with-unusual-initiator-trnas-and-initiation-codons-in-mycoplasmas
#13
Shreya Ahana Ayyub, Divya Dobriyal, Riyaz Ahmad Shah, Kuldeep Lahry, Madhumita Bhattacharyya, Souvik Bhattacharyya, Saikat Chakrabarti, Umesh Varshney
Initiator tRNAs (i-tRNAs) are characterized by the presence of three consecutive GC base pairs (GC/GC/GC) in their anticodon stems in all domains of life. However, many mycoplasmas possess unconventional i-tRNAs wherein the highly conserved sequence of GC/GC/GC is represented by AU/GC/GC, GC/GC/GU or AU/GC/GU. These mycoplasmas also tend to preferentially utilize non-AUG initiation codons. To investigate if initiation with the unconventional i-tRNAs and non-AUG codons in mycoplasmas correlated with the changes in the other components of the translation machinery, we carried out multiple sequence alignments of genes encoding initiation factors (IF), 16S rRNAs, and the ribosomal proteins such as uS9, uS12 and uS13...
September 13, 2017: RNA Biology
https://www.readbyqxmd.com/read/28899630/protection-against-infectious-bronchitis-virus-by-spike-ectodomain-subunit-vaccine
#14
Fatma Eldemery, Kellye S Joiner, Haroldo Toro, Vicky L van Santen
The avian coronavirus infectious bronchitis virus (IBV) S1 subunit of the spike (S) glycoprotein mediates viral attachment to host cells and the S2 subunit is responsible for membrane fusion. Using IBV Arkansas-type (Ark) S protein histochemistry, we show that extension of S1 with the S2 ectodomain improves binding to chicken tissues. Although the S1 subunit is the major inducer of neutralizing antibodies, vaccination with S1 protein has been shown to confer inadequate protection against challenge. The demonstrated contribution of S2 ectodomain to binding to chicken tissues suggests that vaccination with the ectodomain might improve protection compared to vaccination with S1 alone...
September 9, 2017: Vaccine
https://www.readbyqxmd.com/read/28895884/interaction-of-recombinant-gallus-gallus-sept5-and-brain-proteins-of-h5n1-avian-influenza-virus-infected-chickens
#15
Jasmine Elanie Khairat, Vinod Balasubramaniam, Iekhsan Othman, Abdul Rahman Omar, Sharifah Syed Hassan
Septin forms a conserved family of cytoskeletal guanosine triphosphate (GTP) binding proteins that have diverse roles in protein scaffolding, vesicle trafficking, and cytokinesis. The involvement of septins in infectious viral disease pathogenesis has been demonstrated by the upregulation of SEPT5 protein and its mRNA in brain tissues of H5N1-infected chickens, thus, providing evidence for the potential importance of this protein in the pathogenesis of neurovirulence caused by the avian influenza virus. In this study, cloning, expression, and purification of Gallus gallus SEPT5 protein was performed in Escherichia coli...
September 12, 2017: Proteomes
https://www.readbyqxmd.com/read/28882107/statistical-classifiers-for-diagnosing-disease-from-immune-repertoires-a-case-study-using-multiple-sclerosis
#16
Jared Ostmeyer, Scott Christley, William H Rounds, Inimary Toby, Benjamin M Greenberg, Nancy L Monson, Lindsay G Cowell
BACKGROUND: Deep sequencing of lymphocyte receptor repertoires has made it possible to comprehensively profile the clonal composition of lymphocyte populations. This opens the door for novel approaches to diagnose and prognosticate diseases with a driving immune component by identifying repertoire sequence patterns associated with clinical phenotypes. Indeed, recent studies support the feasibility of this, demonstrating an association between repertoire-level summary statistics (e.g., diversity) and patient outcomes for several diseases...
September 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28877774/complete-mitochondrial-genome-of-bamboo-grasshopper-ceracris-fasciata-and-the-phylogenetic-analyses-and-divergence-time-estimation-of-caelifera-orthoptera
#17
S Gao, J J Chen, G F Jiang
The bamboo grasshopper Ceracris fasciata is regarded as a major pest species because of the damage it causes to bamboo, and its classification within the families and subfamilies of the suborder Caelifera remains unclear. Thus, we attempted to resolve these questions using molecular biology methods and analyses. Our results are as follows: (1) the complete mitochondrial genome of C. fasciata is 15,569 bp in length. The mitochondrial genome contains a standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and an A + T-rich region in the same order as those of the other analysed Caeliferan species...
September 7, 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/28876033/-high-level-expression-and-characterization-of-selenomonas-ruminantium-%C3%AE-xylosidase-in-pichia-pastoris
#18
Tingting Fu, Wei Hu, Yong Chen, Huan Wei, Guang Yang
β-xylosidase (EC 3.2.1.37) is an important part of the xylanolytic enzymes system. In the present research, β-xylosidase gene Sxa derived from Selenomonas ruminantium was expressed in Pichia pastoris GS115. According to the codon bias and rare codons of P. pastoris, mRNA secondary structure and GC content, Sxa gene was optimized. The optimized full-length gene mSxa was obtained by gene synthesis technique and the recombinant yeast expression vector pPIC9K-mSxa was constructed. After being digested by restriction enzyme BglⅡ, the mSxa gene was transformed into P...
May 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28871265/expression-of-a-chimeric-gene-encoding-insecticidal-crystal-protein-cry1aabc-of-bacillus-thuringiensis-in-chickpea-cicer-arietinum-l-confers-resistance-to-gram-pod-borer-helicoverpa-armigera-hubner
#19
Alok Das, Subhojit Datta, Shallu Thakur, Alok Shukla, Jamal Ansari, G K Sujayanand, Sushil K Chaturvedi, P A Kumar, N P Singh
Domain swapping and generation of chimeric insecticidal crystal protein is an emerging area of insect pest management. The lepidopteran insect pest, gram pod borer (Helicoverpa armigera H.) wreaks havoc to chickpea crop affecting production. Lepidopteran insects were reported to be controlled by Bt (cryI) genes. We designed a plant codon optimized chimeric Bt gene (cry1Aabc) using three domains from three different cry1A genes (domains I, II, and III from cry1Aa, cry1Ab, and cry1Ac, respectively) and expressed it under the control of a constitutive promoter in chickpea (cv...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28865429/a-new-and-updated-resource-for-codon-usage-tables
#20
John Athey, Aikaterini Alexaki, Ekaterina Osipova, Alexandre Rostovtsev, Luis V Santana-Quintero, Upendra Katneni, Vahan Simonyan, Chava Kimchi-Sarfaty
BACKGROUND: Due to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codons may affect protein expression, structure, and function. Recombinant gene technologies commonly take advantage of the former effect by implementing a technique termed codon optimization, in which codons are replaced with synonymous ones in order to increase protein expression...
September 2, 2017: BMC Bioinformatics
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