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Dna-encoded library

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https://www.readbyqxmd.com/read/27916887/cucumber-metallothionein-like-2-csmtl2-exhibits-metal-binding-properties
#1
Yu Pan, Yanglu Pan, Junpeng Zhai, Yan Xiong, Jinhua Li, Xiaobing Du, Chenggang Su, Xingguo Zhang
We identified a novel member of the metallothionein (MT) family, Cucumis sativus metallothionein-like 2 (CsMTL2), by screening a young cucumber fruit complementary DNA (cDNA) library. The CsMTL2 encodes a putative 77-amino acid Class II MT protein that contains two cysteine (Cys)-rich domains separated by a Cys-free spacer region. We found that CsMTL2 expression was regulated by metal stress and was specifically induced by Cd(2+) treatment. We investigated the metal-binding characteristics of CsMTL2 and its possible role in the homeostasis and/or detoxification of metals by heterologous overexpression in Escherichia coli cells...
November 30, 2016: Genes
https://www.readbyqxmd.com/read/27915375/identification-of-enzymes-responsible-for-extracellular-alginate-depolymerization-and-alginate-metabolism-in-vibrio-algivorus
#2
Hidetaka Doi, Yuriko Tokura, Yukiko Mori, Kenichi Mori, Yoko Asakura, Yoshihiro Usuda, Hiroo Fukuda, Akito Chinen
Alginate is a marine non-food-competing polysaccharide that has potential applications in biorefinery. Owing to its large size (molecular weight >300,000 Da), alginate cannot pass through the bacterial cell membrane. Therefore, bacteria that utilize alginate are presumed to have an enzyme that degrades extracellular alginate. Recently, Vibrio algivorus sp. SA2(T) was identified as a novel alginate-decomposing and alginate-utilizing species. However, little is known about the mechanism of alginate degradation and metabolism in this species...
December 3, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27905914/development-of-a-gene-synthesis-platform-for-the-efficient-large-scale-production-of-small-genes-encoding-animal-toxins
#3
Ana Filipa Sequeira, Joana L A Brás, Catarina I P D Guerreiro, Renaud Vincentelli, Carlos M G A Fontes
BACKGROUND: Gene synthesis is becoming an important tool in many fields of recombinant DNA technology, including recombinant protein production. De novo gene synthesis is quickly replacing the classical cloning and mutagenesis procedures and allows generating nucleic acids for which no template is available. In addition, when coupled with efficient gene design algorithms that optimize codon usage, it leads to high levels of recombinant protein expression. RESULTS: Here, we describe the development of an optimized gene synthesis platform that was applied to the large scale production of small genes encoding venom peptides...
December 1, 2016: BMC Biotechnology
https://www.readbyqxmd.com/read/27905174/zirconium-iv-catalyzed-ring-opening-of-on-dna-epoxides-in-water
#4
Lijun Fan, Christopher P Davie
DNA-encoded library technology (ELT) has spurred wide interest in the pharmaceutical industry as a powerful tool for hit and lead generation. In recent years a number of "DNA-compatible" chemical modifications have been published and used to synthesize vastly diverse screening libraries. Herein we report a newly developed, zirconium tetrakis(dodecyl sulfate) [Zr(DS)4] catalyzed ring-opening of on-DNA epoxides in water with amines, including anilines. Subsequent cyclization of the resulting on-DNA β-amino alcohols leads to a variety of biologically interesting, non-aromatic heterocycles...
November 30, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#5
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27877178/an-s-adenosyl-methionine-synthetase-sams-gene-from-andropogon-virginicus-l-confers-aluminum-stress-tolerance-and-facilitates-epigenetic-gene-regulation-in-arabidopsis-thaliana
#6
Bunichi Ezaki, Aiko Higashi, Norie Nanba, Takumi Nishiuchi
Candidate clones which conferred Al tolerance to yeast transformants (TFs) were obtained from a cDNA library derived from a highly Al-tolerant poaceae, Andropogon virginicus L. One such clone, AL3A-4, encoded an S-adenosyl methionine synthetase (SAMS) gene. A full-length cDNA was obtained by 5'-RACE, designated AvSAMS1, and introduced into Arabidopsis thaliana to investigate its biological functions under Al stress. Two TF plant lines both showed higher tolerance than the Col-0 ecotype (non-TF) not only for Al stress, but also for Cu, Pb, Zn and diamide stresses, suggesting the AvSAMS1 was a multiple tolerance gene...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27864515/discovery-of-cofactor-specific-bactericidal-mycobacterium-tuberculosis-inha-inhibitors-using-dna-encoded-library-technology
#7
Holly H Soutter, Paolo Centrella, Matthew A Clark, John W Cuozzo, Christoph E Dumelin, Marie-Aude Guie, Sevan Habeshian, Anthony D Keefe, Kaitlyn M Kennedy, Eric A Sigel, Dawn M Troast, Ying Zhang, Andrew D Ferguson, Gareth Davies, Eleanor R Stead, Jason Breed, Prashanti Madhavapeddi, Jon A Read
Millions of individuals are infected with and die from tuberculosis (TB) each year, and multidrug-resistant (MDR) strains of TB are increasingly prevalent. As such, there is an urgent need to identify novel drugs to treat TB infections. Current frontline therapies include the drug isoniazid, which inhibits the essential NADH-dependent enoyl-acyl-carrier protein (ACP) reductase, InhA. To inhibit InhA, isoniazid must be activated by the catalase-peroxidase KatG. Isoniazid resistance is linked primarily to mutations in the katG gene...
November 18, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27845324/boosting-functionality-of-synthetic-dna-circuits-with-tailored-deactivation
#8
Kevin Montagne, Guillaume Gines, Teruo Fujii, Yannick Rondelez
Molecular programming takes advantage of synthetic nucleic acid biochemistry to assemble networks of reactions, in vitro, with the double goal of better understanding cellular regulation and providing information-processing capabilities to man-made chemical systems. The function of molecular circuits is deeply related to their topological structure, but dynamical features (rate laws) also play a critical role. Here we introduce a mechanism to tune the nonlinearities associated with individual nodes of a synthetic network...
November 15, 2016: Nature Communications
https://www.readbyqxmd.com/read/27785541/identification-of-novel-toluene-monooxygenase-genes-in-a-hydrocarbon-polluted-sediment-using-sequence-and-function-based-screening-of-metagenomic-libraries
#9
E Bouhajja, M McGuire, M R Liles, G Bataille, S N Agathos, I F George
The microbial potential for toluene degradation within sediments from a tar oil-contaminated site in Flingern, Germany, was assessed using a metagenomic approach. High molecular weight environmental DNA from contaminated sediments was extracted, purified, and cloned into fosmid and BAC vectors and transformed into Escherichia coli. The fosmid library was screened by hybridization with a PCR amplicon of the α-subunit of the toluene 4-monooxygenase gene to identify genes and pathways encoding toluene degradation...
October 26, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27768949/biofuel-metabolic-engineering-with-biosensors
#10
Stacy-Anne Morgan, Dana C Nadler, Rayka Yokoo, David F Savage
Metabolic engineering offers the potential to renewably produce important classes of chemicals, particularly biofuels, at an industrial scale. DNA synthesis and editing techniques can generate large pathway libraries, yet identifying the best variants is slow and cumbersome. Traditionally, analytical methods like chromatography and mass spectrometry have been used to evaluate pathway variants, but such techniques cannot be performed with high throughput. Biosensors - genetically encoded components that actuate a cellular output in response to a change in metabolite concentration - are therefore a promising tool for rapid and high-throughput evaluation of candidate pathway variants...
October 18, 2016: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/27734375/protocols-for-screening-peptide-motifs-binding-to-ccn-family-proteins
#11
Satoshi Kubota, Harumi Kawaki, Masaharu Takigawa
Function of CCN family proteins is determined by the interactions with multiple cofactors that are present in microenvironment. Therefore, finding out these cofactors is critically important in understanding the molecular function of the CCN family members. For this objective, bacteriophage random peptide display library is a quite feasible tool. In this library, each filamentous bacteriophage is designed to display an oligopeptide of random 12-16 amino acid residues on its surface. Bacteriophage clones that possess the peptides that bind to a CCN family protein are selected through several cycles of a process designated biopanning or affinity selection...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27722597/cyclodextrin-based-facial-amphiphiles-assessing-the-impact-of-the-hydrophilic-lipophilic-balance-in-the-self-assembly-dna-complexation-and-gene-delivery-capabilities
#12
Iris Pflueger, Coralie Charrat, Carmen Ortiz Mellet, José M García Fernández, Christophe Di Giorgio, Juan M Benito
Exhaustive structure-efficacy relationship studies on nonviral gene delivery systems are often hampered by the ill-defined or polydisperse nature of the formulations. Facial amphiphiles based on rigid cage-type molecular scaffolds offer unique possibilities towards these studies. Taking advantage of regioselective functionalization schemes, we have synthesized a library of cationic cyclodextrin (CD) derivatives combining a range of hydrophilic and lipophilic domains. We have scrutinized how the hydrophilic-lipophilic balance (HLB) around the CD scaffold determines their self-assembly capabilities and the DNA binding and release abilities of the corresponding CD : DNA nanocomplexes (CDplexes)...
October 5, 2016: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/27717304/je-a-versatile-suite-to-handle-multiplexed-ngs-libraries-with-unique-molecular-identifiers
#13
Charles Girardot, Jelle Scholtalbers, Sajoscha Sauer, Shu-Yi Su, Eileen E M Furlong
BACKGROUND: The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequencing, different barcodes can be inserted at each fragment end to either increase the number of multiplexed samples in the library or to use one of the barcodes as UMI...
October 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27672049/in-vitro-evolution-of-phi29-dna-polymerase-using-isothermal-compartmentalized-self-replication-technique
#14
Tadas Povilaitis, Gediminas Alzbutas, Rasa Sukackaite, Juozas Siurkus, Remigijus Skirgaila
Compartmentalized self replication (CSR) is widely used for in vitro evolution of thermostable DNA polymerases able to perform PCR in emulsion. We have modified and adapted CSR technique for isothermal DNA amplification using mezophilic phi29 DNA polymerase and whole genome amplification (WGA) reaction. In standard CSR emulsified bacterial cells are disrupted during denaturation step (94-96°C) in the first circles of PCR. Released plasmid DNA that encodes target polymerase and the thermophilic enzyme complement the emulsified PCR reaction mixture and start polymerase gene amplification...
December 2016: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/27671933/basic-a-simple-and-accurate-modular-dna-assembly-method
#15
Marko Storch, Arturo Casini, Ben Mackrow, Tom Ellis, Geoff S Baldwin
Biopart Assembly Standard for Idempotent Cloning (BASIC) is a simple, accurate, and robust DNA assembly method. The method is based on linker-mediated DNA assembly and provides highly accurate DNA assembly with 99 % correct assemblies for four parts and 90 % correct assemblies for seven parts [1]. The BASIC standard defines a single entry vector for all parts flanked by the same prefix and suffix sequences and its idempotent nature means that the assembled construct is returned in the same format. Once a part has been adapted into the BASIC format it can be placed at any position within a BASIC assembly without the need for reformatting...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27671932/speedygenes-exploiting-an-improved-gene-synthesis-method-for-the-efficient-production-of-synthetic-protein-libraries-for-directed-evolution
#16
Andrew Currin, Neil Swainston, Philip J Day, Douglas B Kell
Gene synthesis is a fundamental technology underpinning much research in the life sciences. In particular, synthetic biology and biotechnology utilize gene synthesis to assemble any desired DNA sequence, which can then be incorporated into novel parts and pathways. Here, we describe SpeedyGenes, a gene synthesis method that can assemble DNA sequences with greater fidelity (fewer errors) than existing methods, but that can also be used to encode extensive, statistically designed sequence variation at any position in the sequence to create diverse (but accurate) variant libraries...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27643718/correction-to-dna-compatible-multistep-synthesis-and-applications-to-dna-encoded-libraries
#17
Alexander Lee Satz, Jianping Cai, Yi Chen, Robert Goodnow, Felix Gruber, Agnieszka Kowalczyk, Ann Petersen, Goli Naderi-Oboodi, Lucja Orzechowski, Quentin Strebel
No abstract text is available yet for this article.
September 19, 2016: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/27632947/characterization-of-pseudomonas-aeruginosa-phage-k5-genome-and-identification-of-its-receptor-related-genes
#18
Lingyan Li, Xuewei Pan, Xiaoli Cui, Qinghui Sun, Xiaojing Yang, Hongjiang Yang
Phage genomic information and the nature of host-phage interactions are important for phage applications. In this study, Pseudomonas aeruginosa phage K5 is characterized as a linear double-stranded genomic DNA molecule of 93,754 bp with identical 1182-bp direct terminal repeats. Comparative genomic analysis reveals that phage K5 is highly homologous to the "PaP1-like" phages. Thirteen mutants resistant to phage K5 are screened in a transposon mutant library. The disrupted genetic loci are identified as gene Y880_RS05480 encoding a putative O-antigen polymerase Wzy and gene wapH encoding a glycosyltransferase...
December 2016: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/27612661/directed-evolution-of-glutathione-transferases-towards-a-selective-glutathione-binding-site-and-improved-oxidative-stability
#19
Irine Axarli, Abdi W Muleta, Evangelia G Chronopoulou, Anastassios C Papageorgiou, Nikolaos E Labrou
BACKGROUND: Glutathione transferases (GSTs) are a family of detoxification enzymes that catalyze the conjugation of glutathione (GSH) to electrophilic compounds. METHODS: A library of alpha class GSTs was constructed by DNA shuffling using the DNA encoding the human glutathione transferase A1-1 (hGSTA1-1) and the rat glutathione transferase A1-1 (rGSTA1-1). RESULTS: Activity screening of the library allowed the selection of a chimeric enzyme variant (GSTD4) that displayed high affinity towards GSH and GSH-Sepharose affinity adsorbent, higher kcat/Km and improved thermal stability, compared to the parent enzymes...
September 7, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27609584/-construction-of-anti-b7-h4-scfv-library-and-screening-and-identification-of-anti-b7-h4-scfv
#20
Luanluan Shao, Chaochao Xu, Hongshuai Ji, Weiping Mao, Yingying Wang, Xiaoqian Liu, Yanyan Zhu
Objective To construct the ribosome display library of anti-B7-H4 extracellular domain, and select the antibody with high specificity. Methods The cDNA of B7-H4 extracellular domain was amplified from A549 cells by reverse transcription PCR (RT-PCR). To express ectodomains of B7-H4, the sequence of B7-H4 gene, which encodes the B7-H4 extracellular domains, was inserted into plasmid pET-28a(+). The purified recombinant protein of B7-H4 extracellular domain was used to immunize BALB/c mice. The total RNA was extracted from the spleen of BALB/c mice which had been immunized with B7-H4 recombinant protein...
September 2016: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
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