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Dna-encoded library

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https://www.readbyqxmd.com/read/28607440/an-arabidopsis-mutant-with-high-operating-efficiency-of-photosystem-ii-and-low-chlorophyll-fluorescence
#1
Niels van Tol, Martijn Rolloos, Dieuwertje Augustijn, A Alia, Huub J de Groot, Paul J J Hooykaas, Bert J van der Zaal
The overall light energy to biomass conversion efficiency of plant photosynthesis is generally regarded as low. Forward genetic screens in Arabidopsis have yielded very few mutants with substantially enhanced photochemistry. Here, we report the isolation of a novel Arabidopsis mutant with a high operating efficiency of Photosystem II (φPSII) and low chlorophyll fluorescence from a library of lines harboring T-DNA constructs encoding artificial transcription factors. This mutant was named Low Chlorophyll Fluorescence 1 (LCF1)...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28600885/immunolocalization-of-tar-dna-binding-protein-of-43%C3%A2-kda-tdp-43-in-mouse-seminiferous-epithelium
#2
Hari Prasad Osuru, Patcharin Pramoonjago, Mayuresh Abhyankar, Eric Swanson, LaToya Ann Roker, Helen Cathro, Prabhakara P Reddi
TDP-43 (TAR DNA-binding protein of 43 kDa) is an evolutionarily conserved, ubiquitously expressed, multi-functional DNA/RNA-binding protein with roles in gene transcription, mRNA splicing, stability, transport, micro RNA biogenesis, and suppression of transposons. Aberrant expression of TDP-43 in testis and sperm was recently shown to be associated with male infertility, which highlights the need to understand better the expression of TDP-43 in the testis. We previously cloned TDP-43 from a mouse testis cDNA library, and showed that it functions as a transcriptional repressor, and regulates the precise spatiotemporal expression of the Acrv1 gene, which encodes the acrosomal protein SP-10, during spermatogenesis...
June 10, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/28597662/chitosan-hyaluronic-acid-nanoparticles-rational-design-revisited-for-rna-delivery
#3
Enrique Lallana, Julio M Rios de la Rosa, Annalisa Tirella, Maria Pelliccia, Arianna Gennari, Ian J Stratford, Sanyogitta Puri, Marianne Ashford, Nicola Tirelli
Chitosan/hyaluronic acid (HA) nanoparticles can be used to deliver an RNA/DNA cargo to cells overexpressing HA receptors such as CD44. For these systems, unequivocal links have not been established yet between chitosan macromolecular (molecular weight; degree of deacetylation, i.e., charge density) and nanoparticle variables (complexation strength, i.e., stability; nucleic acid protection; internalization rate) on one hand, and transfection efficiency on the other hand. Here, we have focused on the role of avidity on transfection efficiency in the CD44-expressing HCT-116 as a cellular model; we have employed two differently sized payloads (a large luciferase-encoding mRNA and a much smaller anti-Luc siRNA), and a small library of chitosans (variable molecular weight and degree of deactylation)...
June 19, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28596758/a-functional-metagenomic-analysis-of-tetracycline-resistance-in-cheese-bacteria
#4
Ana B Flórez, Lucía Vázquez, Baltasar Mayo
Metagenomic techniques have been successfully used to monitor antibiotic resistance genes in environmental, animal and human ecosystems. However, despite the claim that the food chain plays a key role in the spread of antibiotic resistance, metagenomic analysis has scarcely been used to investigate food systems. The present work reports a functional metagenomic analysis of the prevalence and evolution of tetracycline resistance determinants in a raw-milk, blue-veined cheese during manufacturing and ripening...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28593475/functional-metagenomics-of-oil-impacted-mangrove-sediments-reveals-high-abundance-of-hydrolases-of-biotechnological-interest
#5
Júlia Ronzella Ottoni, Lucélia Cabral, Sanderson Tarciso Pereira de Sousa, Gileno Vieira Lacerda Júnior, Daniela Ferreira Domingos, Fábio Lino Soares Junior, Mylenne Calciolari Pinheiro da Silva, Joelma Marcon, Armando Cavalcante Franco Dias, Itamar Soares de Melo, Anete Pereira de Souza, Fernando Dini Andreote, Valéria Maia de Oliveira
Mangroves are located in coastal wetlands and are susceptible to the consequences of oil spills, what may threaten the diversity of microorganisms responsible for the nutrient cycling and the consequent ecosystem functioning. Previous reports show that high concentration of oil favors the incidence of epoxide hydrolases and haloalkane dehalogenases in mangroves. This finding has guided the goals of this study in an attempt to broaden the analysis to other hydrolases and thereby verify whether oil contamination interferes with the prevalence of particular hydrolases and their assigned microorganisms...
July 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28581718/ruthenium-promoted-on-dna-ring-closing-metathesis-and-cross-metathesis
#6
Xiaojie Lu, Lijun Fan, Christopher B Phelps, Christopher P Davie, Christine P Donahue
DNA-encoded library technology (ELT) is now widely used in pharmaceutical, biotechnological, and academic research for hit identification and target validation. New on-DNA reactions are keys to exploring greater chemical space and accessing challenging chemotypes such as configurationally constrained macrocycles. Herein, we describe the first on-DNA ring-closing metathesis (RCM) and cross-metathesis (CM) reactions promoted by fast initiating Grubbs Ru reagents. Under the optimized conditions, MgCl2 was used to protect the DNA from Ru-induced decomposition...
June 21, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28553854/characteristics-of-yak-platelet-derived-growth-factors-alpha-gene-and-expression-in-brain-tissues
#7
Zhenhua Huang, Yangyang Pan, Penggang Liu, Sijiu Yu, Yan Cui
BACKGROUND: Platelet derived growth factors (PDGFs) are key components of autocrine and paracrine signaling, both of which play important roles in mammalian developmental processes. PDGF expression levels also relate to oxygen levels. The characteristics of yak PDGFs, which are indigenous to hypoxic environments, have not been clearly described until the current study. MATERIALS AND METHODS: We amplified the open reading frame encoding yak (Bos grunniens) platelet derived growth factor-a (PDGFA) from a yak skin tissue cDNA library by reverse transcriptase polymerase chain reaction (PCR) using specific primers and Sanger dideoxy sequencing...
May 29, 2017: Folia Morphologica (Warsz)
https://www.readbyqxmd.com/read/28542326/the-murine-cytomegalovirus-m35-protein-antagonizes-type-i-ifn-induction-downstream-of-pattern-recognition-receptors-by-targeting-nf-%C3%AE%C2%BAb-mediated-transcription
#8
Baca Chan, Vladimir Gonçalves Magalhães, Niels A W Lemmermann, Vanda Juranić Lisnić, Markus Stempel, Kendra A Bussey, Elisa Reimer, Jürgen Podlech, Stefan Lienenklaus, Matthias J Reddehase, Stipan Jonjić, Melanie M Brinkmann
The type I interferon (IFN) response is imperative for the establishment of the early antiviral immune response. Here we report the identification of the first type I IFN antagonist encoded by murine cytomegalovirus (MCMV) that shuts down signaling following pattern recognition receptor (PRR) sensing. Screening of an MCMV open reading frame (ORF) library identified M35 as a novel and strong negative modulator of IFNβ promoter induction following activation of both RNA and DNA cytoplasmic PRR. Additionally, M35 inhibits the proinflammatory cytokine response downstream of Toll-like receptors (TLR)...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28531348/plant-derived-transcription-factors-for-orthologous-regulation-of-gene-expression-in-the-yeast-saccharomyces-cerevisiae
#9
Gita Naseri, Salma Balazadeh, Fabian Machens, Iman Kamranfar, Katrin Messerschmidt, Bernd Mueller-Roeber
Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects for which a tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harboring cognate cis-regulatory motifs driving a yEGFP reporter...
June 9, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28523377/mining-lipolytic-enzymes-in-community-dna-from-high-andean-soils-using-a-targeted-approach
#10
Daniel Borda-Molina, José Salvador Montaña, María Mercedes Zambrano, Sandra Baena
Microbial enrichments cultures are a useful strategy to speed up the search for enzymes that can be employed in industrial processes. Lipases have gained special attention because they show unique properties such as: broad substrate specificity, enantio- and regio-selectivity and stability in organic solvents. A major goal is to identify novel lipolytic enzymes from microorganisms living in cold extreme environments such as high Andean soils, of relevance to our study being their capability be used in industrial processes...
May 18, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28507705/acid-and-au-i-mediated-synthesis-of-hexathymidine-dna-heterocycle-chimeras-an-efficient-entry-to-dna-encoded-libraries-inspired-by-drug-structures
#11
Mateja Klika Škopić, Hazem Salamon, Olivia Bugain, Kathrin Jung, Anne Gohla, Lara J Doetsch, Denise Dos Santos, Avinash Bhat, Bernd Wagner, Andreas Brunschweiger
Libraries of DNA-tagged compounds are a validated screening technology for drug discovery. They are synthesized through combinatorial iterations of alternated coding and preparative synthesis steps. Thus, large chemical space can be accessed for target-based screening. However, the need to preserve the functionality of the DNA tag severely restricts the choice of chemical methods for library synthesis. Acidic organocatalysts, transition metals, and oxidants furnish diverse drug-like structures from simple starting materials, but cause loss of genetic information by depurination...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28487680/diversity-of-metabolically-active-bacteria-in-water-flooded-high-temperature-heavy-oil-reservoir
#12
Tamara N Nazina, Natalya M Shestakova, Ekaterina M Semenova, Alena V Korshunova, Nadezda K Kostrukova, Tatiana P Tourova, Liu Min, Qingxian Feng, Andrey B Poltaraus
The goal of this work was to study the overall genomic diversity of microorganisms of the Dagang high-temperature oilfield (PRC) and to characterize the metabolically active fraction of these populations. At this water-flooded oilfield, the microbial community of formation water from the near-bottom zone of an injection well where the most active microbial processes of oil degradation occur was investigated using molecular, cultural, radiotracer, and physicochemical techniques. The samples of microbial DNA and RNA from back-flushed water were used to obtain the clone libraries for the 16S rRNA gene and cDNA of 16S rRNA, respectively...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28486658/a-high-coverage-draft-genome-of-the-mycalesine-butterfly-bicyclus-anynana
#13
Reuben W Nowell, Ben Elsworth, Vicencio Oostra, Bas J Zwaan, Christopher W Wheat, Marjo Saastamoinen, Ilik J Saccheri, Arjen E Van't Hof, Bethany R Wasik, Heidi Connahs, Muhammad L Aslam, Sujai Kumar, Richard J Challis, Antónia Monteiro, Paul M Brakefield, Mark Blaxter
Background: The mycalesine butterfly Bicyclus anynana , the 'Squinting bush brown', is a model organism in the study of lepidopteran ecology, development and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Findings: Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology...
May 9, 2017: GigaScience
https://www.readbyqxmd.com/read/28485044/a-specific-and-covalent-jnk-1-ligand-selected-from-an-encoded-self-assembling-chemical-library
#14
Gunther Zimmermann, Ulrike Rieder, Davor Bajic, Sara Vanetti, Apirat Chaikuad, Stefan Knapp, Jörg Scheuermann, Martin Mattarella, Dario Neri
We describe the construction of a DNA-encoded chemical library comprising 148 135 members, generated through the self-assembly of two sub-libraries, containing 265 and 559 members, respectively. The library was designed to contain building blocks potentially capable of forming covalent interactions with target proteins. Selections performed with JNK1, a kinase containing a conserved cysteine residue close to the ATP binding site, revealed the preferential enrichment of a 2-phenoxynicotinic acid moiety (building block A82) and a 4-(3,4-difluorophenyl)-4-oxobut-2-enoic acid moiety (building block B272)...
May 9, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28446605/crispr-cas9-mediated-gene-knockout-screens-and-target-identification-via-whole-genome-sequencing-uncover-host-genes-required-for-picornavirus-infection
#15
Heon Seok Kim, Kyungjin Lee, Sangsu Bae, Jeongbin Park, Chong-Kyo Lee, Meehyein Kim, Eunji Kim, Minju Kim, Seokjoong Kim, Chonsaeng Kim, Jin-Soo Kim
Several groups have used genome-wide libraries of lentiviruses encoding small-guide RNAs (sgRNAs) for genetic screens. In most cases, sgRNA expression cassettes are integrated into cells by using lentiviruses, and target genes are statistically estimated by the readout of sgRNA sequences after targeted sequencing. We present a new virus-free method for human gene-knockout screens using a genome-wide library of CRISPR/Cas9 sgRNAs based on plasmids, and target gene identification via whole-genome sequencing (WGS) confirming authentic mutations rather than statistical estimating through targeted amplicon sequencing...
April 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28443514/compound-libraries-recent-advances-and-their-applications-in-drug-discovery
#16
Zhen Gong, Guoping Hu, Qiang Li, Zhiguo Liu, Fei Wang, Xuejin Zhang, Jian Xiong, Peng Li, Yan Xu, Rujian Ma, Shuhui Chen, Jian Li
Hit identification is the starting point of small-molecule drug discovery and is therefore very important to the pharmaceutical industry. One of the most important approaches to identify a new hit is to screen a compound library using an in vitro assay. High-throughput screening has made great contributions to drug discovery since the 1990s but requires expensive equipment and facilities, and its success depends on the size of the compound library. Recent progress in the development of compound libraries has provided more efficient ways to identify new hits for novel drug targets, thereby helping to promote the development of the pharmaceutical industry, especially for first-in-class drugs...
April 25, 2017: Current Drug Discovery Technologies
https://www.readbyqxmd.com/read/28441938/mitors-a-method-for-high-throughput-sensitive-and-accurate-detection-of-mitochondrial-dna-heteroplasmy
#17
Julien Marquis, Gregory Lefebvre, Yiannis A I Kourmpetis, Mohamed Kassam, Frédéric Ronga, Umberto De Marchi, Andreas Wiederkehr, Patrick Descombes
BACKGROUND: Mitochondrial dysfunction is linked to numerous pathological states, in particular related to metabolism, brain health and ageing. Nuclear encoded gene polymorphisms implicated in mitochondrial functions can be analyzed in the context of classical genome wide association studies. By contrast, mitochondrial DNA (mtDNA) variants are more challenging to identify and analyze for several reasons. First, contrary to the diploid nuclear genome, each cell carries several hundred copies of the circular mitochondrial genome...
April 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28392906/selection-of-single-chain-variable-fragments-specific-for-mycobacterium-tuberculosis-esat-6-antigen-using-ribosome-display
#18
Shahrzad Ahangarzadeh, Mojgan Bandehpour, Bahram Kazemi
OBJECTIVES: Tuberculosis (TB) is still one of the problematic infectious diseases in developing countries, especially in Iran. In the present study, we applied ribosome display technique to select single chain variable fragments (scFvs) specific for the 6-kDa early secretory antigenic target (ESAT-6) antigen of Mycobacterium tuberculosis from a mouse scFv library. MATERIALS AND METHODS: The gene encoding ESAT-6 was cloned into pET22b(+) plasmid and expressed in Escherichia coli BL21 (DE3)...
March 2017: Iranian Journal of Basic Medical Sciences
https://www.readbyqxmd.com/read/28384204/cloning-expression-and-antioxidant-activity-of-a-thioredoxin-peroxidase-from-branchiostoma-belcheri-tsingtaunese
#19
Jian Liao, Kaiyu Wang, Weirong Yao, Xunfei Yi, Huihui Yan, Min Chen, Xiaopeng Lan
Peroxiredoxins (Prxs) are ubiquitous antioxidant enzymes that catalyze the thioredoxin- dependent reduction of hydroperoxides. In this study, a novel thioredoxin peroxidase (Bbt-TPx1), a member of the peroxiredoxin superfamily, was found by EST sequence analysis of a cDNA library of Branchiostoma belcheri tsingtaunese ovary. The sequence of a full-length cDNA clone contained an open reading frame encoding a polypeptide of 198 amino acid residues, with a calculated molecular weight of 22,150 Da. The expression patterns of the protein at different developmental stages and adult amphioxus tissues indicate that this enzyme may play important roles in anti-oxidation and innate immunity...
2017: PloS One
https://www.readbyqxmd.com/read/28377530/topoisomerase-ii-inhibitors-induce-dna-damage-dependent-interferon-responses-circumventing-ebola-virus-immune-evasion
#20
Priya Luthra, Sebastian Aguirre, Benjamin C Yen, Colette A Pietzsch, Maria T Sanchez-Aparicio, Bersabeh Tigabu, Lorraine K Morlock, Adolfo García-Sastre, Daisy W Leung, Noelle S Williams, Ana Fernandez-Sesma, Alexander Bukreyev, Christopher F Basler
Ebola virus (EBOV) protein VP35 inhibits production of interferon alpha/beta (IFN) by blocking RIG-I-like receptor signaling pathways, thereby promoting virus replication and pathogenesis. A high-throughput screening assay, developed to identify compounds that either inhibit or bypass VP35 IFN-antagonist function, identified five DNA intercalators as reproducible hits from a library of bioactive compounds. Four, including doxorubicin and daunorubicin, are anthracycline antibiotics that inhibit topoisomerase II and are used clinically as chemotherapeutic drugs...
April 4, 2017: MBio
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