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Recombinant DNA

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https://www.readbyqxmd.com/read/28437612/combinatorial-library-based-on-restriction-enzyme-mediated-modular-assembly
#1
Cuiping Ma, Chao Liang, Yifan Wang, Mei Pan, Qianqian Jiang, Chao Shi
Combinatorial approaches in directed evolution were proven to be more efficient for exploring sequence space and innovating the function of protein. We presented modular assembly of secondary structures (MASS) for constructing a combinatorial library. In this approach, secondary structure elements were extracted from natural existing proteins, the common linkers were flanking secondary structure elements, then digested by Hinf I restriction endonuclease that was used in the construction of combinatorial library for the first time...
April 24, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28437139/protection-against-common-bean-rust-conferred-by-a-gene-silencing-method
#2
Bret Cooper, Kimberly B Campbell
Rust disease of the dry bean plant, Phaseolus vulgaris, is caused by the fungus Uromyces appendiculatus. The fungus acquires its nutrients and energy from bean leaves using a specialized cell structure, the haustorium, through which it secretes effector proteins that contribute to pathogenicity by defeating the plant immune system. Candidate effectors have been identified by DNA sequencing and motif analysis, and some candidates have been observed in infected leaves by mass spectrometry. To assess their roles in pathogenicity, we have inserted small fragments of genes for five candidates into bean pod mottle virus...
April 24, 2017: Phytopathology
https://www.readbyqxmd.com/read/28436563/an-in-vitro-system-for-measuring-genotoxicity-mediated-by-human-cyp3a4-in-saccharomyces-cerevisiae
#3
Michael Fasullo, Julian Freedland, Nicholas St John, Cinzia Cera, Patricia Egner, Matthew Hartog, Xinxin Ding
P450 activity is required to metabolically activate many chemical carcinogens, rendering them highly genotoxic. CYP3A4 is the most abundantly expressed P450 enzyme in the liver, accounting for most drug metabolism and constituting 50% of all hepatic P450 activity. CYP3A4 is also expressed in extrahepatic tissues, including the intestine. However, the role of CYP3A4 in activating chemical carcinogens into potent genotoxins is unclear. To facilitate efforts to determine whether CYP3A4, per se, can activate carcinogens into potent genotoxins, we expressed human CYP3A4 in the DNA-repair mutant (rad4 rad51) strain of budding yeast Saccharomyces cerevisiae and tested the novel, recombinant yeast strain for ability to report CYP3A4-mediated genotoxicity of a well-known genotoxin, aflatoxin B1 (AFB1 )...
April 24, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28436335/localization-of-the-werner-protein-together-with-h2ax-in-%C3%AE-irradiation-induced-neoplastic-transformed-human-mesenchymal-stem-cells
#4
Nedime Serakinci, Tufan Cankaya, Steen Kølvraa
The H2A histone family, member X (H2AX), and Werner (WRN) are important proteins for genome and telomere maintenance. WRN has a major role in genome stability, particularly during DNA replication, transcription, recombination, and repair of DNA double-stranded breaks (DSBs) via base excision repair, homologous recombination, or nonhomologous end joining. H2AX plays a part in the rapid, sensitive, cellular response to the ionizing radiation or DNA-damaging chemotherapeutic agents that cause DSBs. This occurs when radiation-induced DSBs trigger the activation of H2AX and begin the damage-repair process...
2017: Critical Reviews in Eukaryotic Gene Expression
https://www.readbyqxmd.com/read/28435519/gt198-psmc3ip-germline-variants-in-early-onset-breast-cancer-patients-from-hereditary-breast-and-ovarian-cancer-families
#5
Stephanie Schubert, Tim Ripperger, Melanie Rood, Anthony Petkidis, Winfried Hofmann, Hildegard Frye-Boukhriss, Marcel Tauscher, Bernd Auber, Ursula Hille-Betz, Thomas Illig, Brigitte Schlegelberger, Doris Steinemann
GT198, located 470 kb downstream of BRCA1, encodes for the nuclear PSMC3-interacting protein, which functions as co-activator of steroid hormone-mediated gene expression, and is involved in RAD51 and DMC1-mediated homologous recombination during DNA repair of double-strand breaks. Recently, germline variants in GT198 have been identified in hereditary breast and ovarian cancer (HBOC) patients, mainly in cases with early-onset. We screened a cohort of 166 BRCA1/2 mutation-negative HBOC patients, of which 56 developed early-onset breast cancer before the age of 36 years, for GT198 variants...
January 2017: Genes & Cancer
https://www.readbyqxmd.com/read/28433722/high-precision-genome-sequencing-of-engineered-g-oxydans-621h-by-combining-long-nanopore-and-short-accurate-illumina-reads
#6
Angela Kranz, Alexander Vogel, Ursula Degner, Ines Kiefler, Michael Bott, Björn Usadel, Tino Polen
State of the art and novel high-throughput DNA sequencing technologies enable fascinating opportunities and applications in the life sciences including microbial genomics. Short high-quality read data already enable not only microbial genome sequencing, yet can be inadequately to solve problems in genome assemblies and for the analysis of structural variants, especially in engineered microbial cell factories. Single-molecule real-time sequencing technologies generating long reads promise to solve such assembly problems...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28432456/deregulated-bcl-2-family-proteins-impact-on-repair-of-dna-double-strand-breaks-and-are-targets-to-overcome-radioresistance-in-lung-cancer
#7
Sarah A Wieczorek, Frank Breitenbuecher, Aashish Soni, Katja Paul-Konietzko, Sophie Ziegler, Ali Sak, George Iliakis, Martin Schuler
PURPOSE: DNA damage-induced cell death is a major effector mechanism of radiotherapy. Aberrant expression of anti-apoptotic BCL-2 family proteins is frequently observed in lung cancers. Against this background, we studied radioresistance mediated by BCL-2 family proteins at the mechanistic level and its potential as target for radiochemotherapy. METHODS: Lung cancer models stably expressing BCL-xL or MCL-1 were irradiated to study cell death, clonogenic survival, and DNA repair kinetics in vitro, and growth suppression of established tumors in vivo...
April 21, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28432121/the-lon-protease-like-domain-in-the-bacterial-reca-paralog-rada-is-required-for-dna-binding-and-repair
#8
Masao Inoue, Kenji Fukui, Yuki Fujii, Noriko Nakagawa, Takato Yano, Seiki Kuramitsu, Ryoji Masui
Homologous recombination (HR) plays an essential role in the maintenance of genome integrity. RecA/Rad51 paralogs have been recognized as an important factor of HR. Among them, only one bacterial RecA/Rad51 paralog - RadA - is involved in HR as an accessory factor of RecA recombinase. RadA has a unique Lon protease-like domain (LonC) at its C-terminus, in addition to a RecA-like ATPase domain. Unlike Lon protease, RadA's LonC domain does not show protease activity but is still essential for RadA-mediated DNA repair...
April 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28432093/diversity-of-integrative-and-conjugative-elements-of-streptococcus-salivarius-and-their-intra-and-interspecies-transfer
#9
Narimane Dahmane, Virginie Libante, Florence Charron-Bourgoin, Eric Guédon, Gérard Guédon, Nathalie Leblond-Bourget, Sophie Payot
Integrative and Conjugative Elements (ICEs) are widespread chromosomal mobile genetic elements, which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3' end of fda, rpsI or rpmG genes) with the conjugation module of the ICESt3 subfamily...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431926/multiple-repair-pathways-mediate-cellular-tolerance-to-resveratrol-induced-dna-damage
#10
Ying Liu, Xiaohua Wu, Xiaoqing Hu, Ziyuan Chen, Hao Liu, Shunichi Takeda, Yong Qing
Resveratrol (RSV) has been reported to exert health benefits for the prevention and treatment of many diseases, including cancer. The anticancer mechanisms of RSV seem to be complex and may be associated with genotoxic potential. To better understand the genotoxic mechanisms, we used wild-type (WT) and a panel of isogenic DNA-repair deficient DT40 cell lines to identify the DNA damage effects and molecular mechanisms of cellular tolerance to RSV. Our results showed that RSV induced significant formation of γ-H2AX foci and chromosome aberrations (CAs) in WT cells, suggesting direct DNA damage effects...
April 18, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28431563/inheritance-of-brewing-relevant-phenotypes-in-constructed-saccharomyces-cerevisiae%C3%A2-%C3%A3-%C3%A2-saccharomyces-eubayanus-hybrids
#11
Kristoffer Krogerus, Tuulikki Seppänen-Laakso, Sandra Castillo, Brian Gibson
BACKGROUND: Interspecific hybridization has proven to be a potentially valuable technique for generating de novo lager yeast strains that possess diverse and improved traits compared to their parent strains. To further enhance the value of hybridization for strain development, it would be desirable to combine phenotypic traits from more than two parent strains, as well as remove unwanted traits from hybrids. One such trait, that has limited the industrial use of de novo lager yeast hybrids, is their inherent tendency to produce phenolic off-flavours; an undesirable trait inherited from the Saccharomyces eubayanus parent...
April 21, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28431522/comparative-proteomic-analysis-of-neisseria-meningitidis-wildtype-and-dpra-null-mutant-strains-links-dna-processing-to-pilus-biogenesis
#12
Getachew Tesfaye Beyene, Shewit Kalayou, Tahira Riaz, Tone Tonjum
BACKGROUND: DNA processing chain A (DprA) is a DNA binding protein which is ubiquitous in bacteria, and is required for DNA transformation to various extents among bacterial species. However, the interaction of DprA with competence and recombination proteins is poorly understood. Therefore, the proteomes of whole Neisseria meningitidis (Nm) wildtype and dprA mutant cells were compared. Such a comparative proteomic analysis increases our understanding of the interactions of DprA with other Nm components and may elucidate its potential role beyond DNA processing in transformation...
April 21, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28431265/nucleolar-reorganization-in-response-to-rdna-damage
#13
REVIEW
Marjolein van Sluis, Brian McStay
Nucleoli, sites of ribosome biogenesis, form around nucleolar organizer regions (NORs) comprising rDNA arrays, located on human acrocentric chromosome p-arms. NORs provide an opportunity to investigate the DNA double strand break (DSB) response at highly transcribed, repetitive, essential loci. Targeted introduction of DSBs into rDNA results in ATM-dependent inhibition of RNA-polymerase I transcription, coupled with movement of rDNA from the nucleolar interior to anchoring points at the periphery. Reorganization renders rDNA accessible to repair factors, normally excluded from nucleoli...
April 18, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28431013/dna-double-strand-break-repair-in-penaeus-monodon-is-predominantly-dependent-on-homologous-recombination
#14
Shikha Srivastava, Sumedha Dahal, Sharanya J Naidu, Deepika Anand, Vidya Gopalakrishnan, Rajendran Kooloth Valappil, Sathees C Raghavan
DNA double-strand breaks (DSBs) are mostly repaired by nonhomologous end joining (NHEJ) and homologous recombination (HR) in higher eukaryotes. In contrast, HR-mediated DSB repair is the major double-strand break repair pathway in lower order organisms such as bacteria and yeast. Penaeus monodon, commonly known as black tiger shrimp, is one of the economically important crustaceans facing large-scale mortality due to exposure to infectious diseases. The animals can also get exposed to chemical mutagens under the culture conditions as well as in wild...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28430197/g-quadruplex-organic-frameworks
#15
Yi-Lin Wu, Noah E Horwitz, Kan-Sheng Chen, Diego A Gomez-Gualdron, Norman S Luu, Lin Ma, Timothy C Wang, Mark C Hersam, Joseph T Hupp, Omar K Farha, Randall Q Snurr, Michael R Wasielewski
Two-dimensional covalent organic frameworks often π stack into crystalline solids that allow precise spatial positioning of molecular building blocks. Inspired by the hydrogen-bonded G-quadruplexes found frequently in guanine-rich DNA, here we show that this structural motif can be exploited to guide the self-assembly of naphthalene diimide and perylene diimide electron acceptors end-capped with two guanine electron donors into crystalline G-quadruplex-based organic frameworks, wherein the electron donors and acceptors form ordered, segregated π-stacked arrays...
May 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28429327/large-scale-cultivation-of-euglena
#16
Kengo Suzuki
From the middle of the twentieth century, microalgae have been exploited as a candidate biomass source of food and other products. One such candidate source is the fast-proliferating microalga Euglena gracilis. The commercial cultivation of E. gracilis began in 2007, after the success of its outdoor mass cultivation and improvement of the harvesting and drying methods suitable for Euglena cells. The commercialization of Euglena production is based on the strategy of "5Fs of Biomass," which refers to the development and production of commercial products including food, fiber, feed, fertilizer, and fuel from biomass...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28429156/crystallization-and-preliminary-x-ray-diffraction-analysis-of-a-mammal-inositol-1-3-4-5-6-pentakisphosphate-2-kinase
#17
Elsa Franco-Echevarría, Julia Sanz-Aparicio, Nathalie Troffer-Charlier, Arnaud Poterszman, Beatriz González
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IP5 2-K) is an enzyme that catalyses the formation of phytic acid (IP6) from IP5 and ATP. In mammals, IP6 is involved in multiple events such as DNA repair and mRNA edit and it is the precursor of inositol pyrophosphates, emerging compounds shown to have an essential role in apoptosis. In addition, IP5 2-K have functions in cells independently of its catalytic activity, for example in rRNA biogenesis. We pursue the structure determination of a mammal IP5 2-K by Protein Crystallography...
April 21, 2017: Protein Journal
https://www.readbyqxmd.com/read/28428799/a-novel-cytoplasmic-male-sterility-in-brassica-napus-inap-cms-with-carpelloid-stamens-via-protoplast-fusion-with-chinese-woad
#18
Lei Kang, Pengfei Li, Aifan Wang, Xianhong Ge, Zaiyun Li
A novel cytoplasmic male sterility (CMS) in Brassica napus (inap CMS) was selected from the somatic hybrid with Isatis indigotica (Chinese woad) by recurrent backcrossing. The male sterility was caused by the conversion of tetradynamous stamens into carpelloid structures with stigmatoid tissues at their tips and ovule-like tissues in the margins, and the two shorter stamens into filaments without anthers. The feminized development of the stamens resulted in the complete lack of pollen grains, which was stable in different years and environments...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28428305/draft-genome-sequence-of-the-plasmid-free-lactococcus-lactis-subsp-lactis-strain-lmg-19460
#19
Inês N Silva, Sofia Duarte, Leonilde M Moreira, Gabriel A Monteiro
We report here the draft genome sequence of the plasmid-free Lactococcus lactis subsp. lactis strain LMG 19460. This strain has potential application for a cost-effective production of food-grade plasmid DNA to use in DNA vaccines, produce recombinant proteins, and be used as a mucosal delivery vehicle of therapeutic molecules.
April 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28427225/enhancing-synthetic-lethality-of-parp-inhibitor-and-cisplatin-in-brca-proficient-tumour-cells-with-hyperthermia
#20
Arlene L Oei, Caspar M van Leeuwen, Vidhula R Ahire, Hans M Rodermond, Rosemarie Ten Cate, Anneke M Westermann, Lukas J A Stalpers, Johannes Crezee, H Petra Kok, Przemek M Krawczyk, Roland Kanaar, Nicolaas A P Franken
BACKGROUND: Poly-(ADP-ribose)-polymerase1 (PARP1) is involved in repair of DNA single strand breaks. PARP1-inhibitors (PARP1-i) cause an accumulation of DNA double strand breaks, which are generally repaired by homologous recombination (HR). Therefore, cancer cells harboring HR deficiencies are exceptionally sensitive to PARP1-i. For patients with HR-proficient tumors, HR can be temporarily inhibited by hyperthermia, thereby inducing synthetic lethal conditions in every tumor type. Since cisplatin is successfully used combined with hyperthermia (thermochemotherapy), we investigated the effectiveness of combining PARP1-i with thermochemotherapy...
March 6, 2017: Oncotarget
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